diff --git a/packages/deparser/__tests__/pretty/__snapshots__/misc-pretty.test.ts.snap b/packages/deparser/__tests__/pretty/__snapshots__/misc-pretty.test.ts.snap
new file mode 100644
index 00000000..02c8c3cd
--- /dev/null
+++ b/packages/deparser/__tests__/pretty/__snapshots__/misc-pretty.test.ts.snap
@@ -0,0 +1,154 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`Pretty Misc SQL formatting should format misc-1: Complex CTE with joins and aggregation (non-pretty) 1`] = `"WITH recent_orders AS (SELECT o.id, o.user_id, o.created_at FROM orders AS o WHERE o.created_at > (now() - '30 days'::interval)), high_value_orders AS (SELECT r.user_id, count(*) AS order_count, sum(oi.price * oi.quantity) AS total_spent FROM recent_orders AS r JOIN order_items AS oi ON r.id = oi.order_id GROUP BY r.user_id) SELECT u.id, u.name, h.total_spent FROM users AS u JOIN high_value_orders AS h ON u.id = h.user_id WHERE h.total_spent > 1000 ORDER BY h.total_spent DESC"`;
+
+exports[`Pretty Misc SQL formatting should format misc-1: Complex CTE with joins and aggregation (pretty) 1`] = `
+"WITH 
+  recent_orders AS (SELECT
+    o.id,
+    o.user_id,
+    o.created_at
+  FROM orders AS o
+  WHERE
+    o.created_at > (now() - '30 days'::interval)),
+  high_value_orders AS (SELECT
+    r.user_id,
+    count(*) AS order_count,
+    sum(oi.price * oi.quantity) AS total_spent
+  FROM recent_orders AS r
+  JOIN order_items AS oi ON r.id = oi.order_id
+  GROUP BY
+    r.user_id)
+SELECT
+  u.id,
+  u.name,
+  h.total_spent
+FROM users AS u
+JOIN high_value_orders AS h ON u.id = h.user_id
+WHERE
+  h.total_spent > 1000
+ORDER BY
+  h.total_spent DESC"
+`;
+
+exports[`Pretty Misc SQL formatting should format misc-2: Window functions with FILTER and GROUPING SETS (non-pretty) 1`] = `"SELECT department, employee_id, count(*) FILTER (WHERE status = 'active') OVER (PARTITION BY department) AS active_count, rank() OVER (PARTITION BY department ORDER BY salary DESC) AS salary_rank FROM employee_status GROUP BY GROUPING SETS (department, (department, employee_id))"`;
+
+exports[`Pretty Misc SQL formatting should format misc-2: Window functions with FILTER and GROUPING SETS (pretty) 1`] = `
+"SELECT
+  department,
+  employee_id,
+  count(*) FILTER (WHERE status = 'active') OVER (PARTITION BY department) AS active_count,
+  rank() OVER (
+    PARTITION BY department
+    ORDER BY salary DESC
+  ) AS salary_rank
+FROM employee_status
+GROUP BY
+  GROUPING SETS (department, (department, employee_id))"
+`;
+
+exports[`Pretty Misc SQL formatting should format misc-3: LATERAL joins with JSON functions (non-pretty) 1`] = `"SELECT u.id, u.name, j.key, j.value FROM users AS u, LATERAL jsonb_each_text(u.preferences) AS j(key, value) WHERE j.key LIKE 'notif_%' AND CAST(j.value AS boolean) = true"`;
+
+exports[`Pretty Misc SQL formatting should format misc-3: LATERAL joins with JSON functions (pretty) 1`] = `
+"SELECT
+  u.id,
+  u.name,
+  j.key,
+  j.value
+FROM users AS u, LATERAL jsonb_each_text(u.preferences) AS j(key, value)
+WHERE
+  j.key LIKE 'notif_%'
+  AND CAST(j.value AS boolean) = true"
+`;
+
+exports[`Pretty Misc SQL formatting should format misc-4: EXISTS with nested subqueries and CASE (non-pretty) 1`] = `"SELECT p.id, p.title, CASE WHEN EXISTS (SELECT 1 FROM reviews AS r WHERE r.product_id = p.id AND r.rating >= 4) THEN 'Popular' ELSE 'Unrated' END AS status FROM products AS p WHERE p.archived = false"`;
+
+exports[`Pretty Misc SQL formatting should format misc-4: EXISTS with nested subqueries and CASE (pretty) 1`] = `
+"SELECT
+  p.id,
+  p.title,
+CASE 
+  WHEN EXISTS (SELECT
+    1
+  FROM reviews AS r
+  WHERE
+    r.product_id = p.id
+    AND r.rating >= 4) THEN 'Popular' 
+  ELSE 'Unrated' 
+END AS status
+FROM products AS p
+WHERE
+  p.archived = false"
+`;
+
+exports[`Pretty Misc SQL formatting should format misc-5: Nested CTEs with type casts and subqueries (non-pretty) 1`] = `"WITH logs AS (SELECT id, CAST(payload AS pg_catalog.json) ->> 'event' AS event, CAST(CAST(payload AS pg_catalog.json) ->> 'ts' AS pg_catalog.timestamp) AS ts FROM event_log WHERE ts > (now() - '7 days'::interval)) SELECT event, count(*) AS freq FROM ( SELECT DISTINCT event, ts::date AS event_day FROM logs ) AS d GROUP BY event ORDER BY freq DESC"`;
+
+exports[`Pretty Misc SQL formatting should format misc-5: Nested CTEs with type casts and subqueries (pretty) 1`] = `
+"WITH 
+logs AS (SELECT
+  id,
+  CAST(payload AS pg_catalog.json) ->> 'event' AS event,
+  CAST(CAST(payload AS pg_catalog.json) ->> 'ts' AS pg_catalog.timestamp) AS ts
+FROM event_log
+WHERE
+  ts > (now() - '7 days'::interval))
+SELECT
+  event,
+  count(*) AS freq
+FROM ( SELECT DISTINCT
+  event,
+  ts::date AS event_day
+FROM logs ) AS d
+GROUP BY
+  event
+ORDER BY
+  freq DESC"
+`;
+
+exports[`Pretty Misc SQL formatting should format misc-6: Complex multi-table joins with nested conditions (non-pretty) 1`] = `"SELECT o.id AS order_id, u.name AS user_name, p.name AS product_name, s.status, sh.shipped_at, r.refund_amount FROM orders AS o JOIN users AS u ON o.user_id = u.id JOIN order_items AS oi ON oi.order_id = o.id JOIN products AS p ON (p.id = oi.product_id AND p.available = true) OR (p.sku = oi.product_sku AND (p.discontinued = false OR p.replacement_id IS NOT NULL)) LEFT JOIN shipping AS sh ON sh.order_id = o.id AND ((sh.carrier = 'UPS' AND sh.tracking_number IS NOT NULL) OR (sh.carrier = 'FedEx' AND sh.shipped_at > (o.created_at + '1 day'::interval))) LEFT JOIN statuses AS s ON s.id = o.status_id AND (s.name <> 'cancelled' OR (s.name = 'cancelled' AND s.updated_at > (now() - '7 days'::interval))) LEFT JOIN refunds AS r ON r.order_id = o.id AND ((r.status = 'approved' AND r.processed_at IS NOT NULL) OR (r.status = 'pending' AND r.requested_at < (now() - '14 days'::interval))) WHERE o.created_at > (now() - '90 days'::interval) AND u.active = true AND (s.status = 'shipped' OR (s.status = 'processing' AND EXISTS (SELECT 1 FROM order_notes AS n WHERE (n.order_id = o.id AND n.note ILIKE '%expedite%')))) ORDER BY o.created_at DESC"`;
+
+exports[`Pretty Misc SQL formatting should format misc-6: Complex multi-table joins with nested conditions (pretty) 1`] = `
+"SELECT
+  o.id AS order_id,
+  u.name AS user_name,
+  p.name AS product_name,
+  s.status,
+  sh.shipped_at,
+  r.refund_amount
+FROM orders AS o
+JOIN users AS u ON o.user_id = u.id
+JOIN order_items AS oi ON oi.order_id = o.id
+JOIN products AS p ON
+  (p.id = oi.product_id
+    AND p.available = true)
+    OR (p.sku = oi.product_sku
+    AND (p.discontinued = false
+    OR p.replacement_id IS NOT NULL))
+LEFT JOIN shipping AS sh ON sh.order_id = o.id
+  AND ((sh.carrier = 'UPS'
+  AND sh.tracking_number IS NOT NULL)
+  OR (sh.carrier = 'FedEx'
+  AND sh.shipped_at > (o.created_at + '1 day'::interval)))
+LEFT JOIN statuses AS s ON s.id = o.status_id
+  AND (s.name <> 'cancelled'
+  OR (s.name = 'cancelled'
+  AND s.updated_at > (now() - '7 days'::interval)))
+LEFT JOIN refunds AS r ON r.order_id = o.id
+  AND ((r.status = 'approved'
+  AND r.processed_at IS NOT NULL)
+  OR (r.status = 'pending'
+  AND r.requested_at < (now() - '14 days'::interval)))
+WHERE
+  o.created_at > (now() - '90 days'::interval)
+  AND u.active = true
+  AND (s.status = 'shipped'
+  OR (s.status = 'processing'
+  AND EXISTS (SELECT
+  1
+FROM order_notes AS n
+WHERE
+  (n.order_id = o.id
+  AND n.note ILIKE '%expedite%'))))
+ORDER BY
+  o.created_at DESC"
+`;
diff --git a/packages/deparser/__tests__/pretty/misc-pretty.test.ts b/packages/deparser/__tests__/pretty/misc-pretty.test.ts
new file mode 100644
index 00000000..734d9e96
--- /dev/null
+++ b/packages/deparser/__tests__/pretty/misc-pretty.test.ts
@@ -0,0 +1,180 @@
+import { deparseSync } from '../../src';
+import { parse } from 'libpg-query';
+import { expectParseDeparse } from '../../test-utils';
+
+describe('Pretty Misc SQL formatting', () => {
+  const misc1Sql = `WITH recent_orders AS (
+  SELECT o.id, o.user_id, o.created_at
+  FROM orders o
+  WHERE o.created_at > NOW() - INTERVAL '30 days'
+), high_value_orders AS (
+  SELECT r.user_id, COUNT(*) AS order_count, SUM(oi.price * oi.quantity) AS total_spent
+  FROM recent_orders r
+  JOIN order_items oi ON r.id = oi.order_id
+  GROUP BY r.user_id
+)
+SELECT u.id, u.name, h.total_spent
+FROM users u
+JOIN high_value_orders h ON u.id = h.user_id
+WHERE h.total_spent > 1000
+ORDER BY h.total_spent DESC`;
+
+  const misc2Sql = `SELECT
+  department,
+  employee_id,
+  COUNT(*) FILTER (WHERE status = 'active') OVER (PARTITION BY department) AS active_count,
+  RANK() OVER (PARTITION BY department ORDER BY salary DESC) AS salary_rank
+FROM employee_status
+GROUP BY GROUPING SETS ((department), (department, employee_id))`;
+
+  const misc3Sql = `SELECT u.id, u.name, j.key, j.value
+FROM users u,
+LATERAL jsonb_each_text(u.preferences) AS j(key, value)
+WHERE j.key LIKE 'notif_%' AND j.value::boolean = true`;
+
+  const misc4Sql = `SELECT p.id, p.title,
+  CASE
+    WHEN EXISTS (
+      SELECT 1 FROM reviews r
+      WHERE r.product_id = p.id AND r.rating >= 4
+    ) THEN 'Popular'
+    ELSE 'Unrated'
+  END AS status
+FROM products p
+WHERE p.archived = false`;
+
+  const misc5Sql = `WITH logs AS (
+  SELECT id, payload::json->>'event' AS event, (payload::json->>'ts')::timestamp AS ts
+  FROM event_log
+  WHERE ts > NOW() - INTERVAL '7 days'
+)
+SELECT event, COUNT(*) AS freq
+FROM (
+  SELECT DISTINCT event, ts::date AS event_day
+  FROM logs
+) d
+GROUP BY event
+ORDER BY freq DESC`;
+
+  const misc6Sql = `SELECT 
+  o.id AS order_id,
+  u.name AS user_name,
+  p.name AS product_name,
+  s.status,
+  sh.shipped_at,
+  r.refund_amount
+FROM orders o
+JOIN users u 
+  ON o.user_id = u.id
+JOIN order_items oi 
+  ON oi.order_id = o.id
+JOIN products p 
+  ON (
+    (p.id = oi.product_id AND p.available = true)
+    OR 
+    (p.sku = oi.product_sku AND (p.discontinued = false OR p.replacement_id IS NOT NULL))
+  )
+LEFT JOIN shipping sh 
+  ON (
+    sh.order_id = o.id 
+    AND (
+      (sh.carrier = 'UPS' AND sh.tracking_number IS NOT NULL)
+      OR 
+      (sh.carrier = 'FedEx' AND sh.shipped_at > o.created_at + INTERVAL '1 day')
+    )
+  )
+LEFT JOIN statuses s 
+  ON s.id = o.status_id 
+  AND (
+    s.name != 'cancelled'
+    OR (s.name = 'cancelled' AND s.updated_at > NOW() - INTERVAL '7 days')
+  )
+LEFT JOIN refunds r 
+  ON r.order_id = o.id 
+  AND (
+    (r.status = 'approved' AND r.processed_at IS NOT NULL)
+    OR 
+    (r.status = 'pending' AND r.requested_at < NOW() - INTERVAL '14 days')
+  )
+WHERE o.created_at > NOW() - INTERVAL '90 days'
+  AND u.active = true
+  AND (
+    s.status = 'shipped' 
+    OR (
+      s.status = 'processing' 
+      AND EXISTS (
+        SELECT 1 FROM order_notes n WHERE n.order_id = o.id AND n.note ILIKE '%expedite%'
+      )
+    )
+  )
+ORDER BY o.created_at DESC`;
+
+  it('should format misc-1: Complex CTE with joins and aggregation (pretty)', async () => {
+    const result = await expectParseDeparse(misc1Sql, { pretty: true });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-1: Complex CTE with joins and aggregation (non-pretty)', async () => {
+    const result = await expectParseDeparse(misc1Sql, { pretty: false });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-2: Window functions with FILTER and GROUPING SETS (pretty)', async () => {
+    const result = await expectParseDeparse(misc2Sql, { pretty: true });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-2: Window functions with FILTER and GROUPING SETS (non-pretty)', async () => {
+    const result = await expectParseDeparse(misc2Sql, { pretty: false });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-3: LATERAL joins with JSON functions (pretty)', async () => {
+    const result = await expectParseDeparse(misc3Sql, { pretty: true });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-3: LATERAL joins with JSON functions (non-pretty)', async () => {
+    const result = await expectParseDeparse(misc3Sql, { pretty: false });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-4: EXISTS with nested subqueries and CASE (pretty)', async () => {
+    const result = await expectParseDeparse(misc4Sql, { pretty: true });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-4: EXISTS with nested subqueries and CASE (non-pretty)', async () => {
+    const result = await expectParseDeparse(misc4Sql, { pretty: false });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-5: Nested CTEs with type casts and subqueries (pretty)', async () => {
+    const result = await expectParseDeparse(misc5Sql, { pretty: true });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-5: Nested CTEs with type casts and subqueries (non-pretty)', async () => {
+    const result = await expectParseDeparse(misc5Sql, { pretty: false });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-6: Complex multi-table joins with nested conditions (pretty)', async () => {
+    const result = await expectParseDeparse(misc6Sql, { pretty: true });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should format misc-6: Complex multi-table joins with nested conditions (non-pretty)', async () => {
+    const result = await expectParseDeparse(misc6Sql, { pretty: false });
+    expect(result).toMatchSnapshot();
+  });
+
+  it('should validate AST equivalence for all misc cases', async () => {
+    const testCases = [misc1Sql, misc2Sql, misc3Sql, misc4Sql, misc5Sql, misc6Sql];
+    
+    for (const sql of testCases) {
+      await expectParseDeparse(sql, { pretty: false });
+      await expectParseDeparse(sql, { pretty: true });
+    }
+  });
+});
diff --git a/packages/deparser/src/deparser.ts b/packages/deparser/src/deparser.ts
index 4fe7f806..169d74c1 100644
--- a/packages/deparser/src/deparser.ts
+++ b/packages/deparser/src/deparser.ts
@@ -993,14 +993,15 @@ export class Deparser implements DeparserVisitor {
     if (node.ctes && node.ctes.length > 0) {
       const ctes = ListUtils.unwrapList(node.ctes);
       if (this.formatter.isPretty()) {
-        const cteStrings = ctes.map(cte => {
+        const cteStrings = ctes.map((cte, index) => {
           const cteStr = this.visit(cte, context);
+          const prefix = index === 0 ? this.formatter.newline() : ',' + this.formatter.newline();
           if (this.containsMultilineStringLiteral(cteStr)) {
-            return this.formatter.newline() + cteStr;
+            return prefix + cteStr;
           }
-          return this.formatter.newline() + this.formatter.indent(cteStr);
+          return prefix + this.formatter.indent(cteStr);
         });
-        output.push(cteStrings.join(','));
+        output.push(cteStrings.join(''));
       } else {
         const cteStrings = ctes.map(cte => this.visit(cte, context));
         output.push(cteStrings.join(', '));
@@ -1333,7 +1334,12 @@ export class Deparser implements DeparserVisitor {
         }
         
         if (windowParts.length > 0) {
-          result += ` OVER (${windowParts.join(' ')})`;
+          if (this.formatter.isPretty() && windowParts.length > 1) {
+            const formattedParts = windowParts.map(part => this.formatter.indent(part));
+            result += ` OVER (${this.formatter.newline()}${formattedParts.join(this.formatter.newline())}${this.formatter.newline()})`;
+          } else {
+            result += ` OVER (${windowParts.join(' ')})`;
+          }
         } else {
           result += ` OVER ()`;
         }
@@ -1977,17 +1983,41 @@ export class Deparser implements DeparserVisitor {
     }
 
     const args = ListUtils.unwrapList(node.args);
-    for (const arg of args) {
-      output.push(this.visit(arg, context));
-    }
+    
+    if (this.formatter.isPretty() && args.length > 0) {
+      for (const arg of args) {
+        const whenClause = this.visit(arg, context);
+        if (this.containsMultilineStringLiteral(whenClause)) {
+          output.push(this.formatter.newline() + whenClause);
+        } else {
+          output.push(this.formatter.newline() + this.formatter.indent(whenClause));
+        }
+      }
 
-    if (node.defresult) {
-      output.push('ELSE');
-      output.push(this.visit(node.defresult, context));
-    }
+      if (node.defresult) {
+        const elseResult = this.visit(node.defresult, context);
+        if (this.containsMultilineStringLiteral(elseResult)) {
+          output.push(this.formatter.newline() + 'ELSE ' + elseResult);
+        } else {
+          output.push(this.formatter.newline() + this.formatter.indent('ELSE ' + elseResult));
+        }
+      }
 
-    output.push('END');
-    return output.join(' ');
+      output.push(this.formatter.newline() + 'END');
+      return output.join(' ');
+    } else {
+      for (const arg of args) {
+        output.push(this.visit(arg, context));
+      }
+
+      if (node.defresult) {
+        output.push('ELSE');
+        output.push(this.visit(node.defresult, context));
+      }
+
+      output.push('END');
+      return output.join(' ');
+    }
   }
 
   CoalesceExpr(node: t.CoalesceExpr, context: DeparserContext): string {
@@ -3555,10 +3585,20 @@ export class Deparser implements DeparserVisitor {
         output.push(`USING (${columnNames.join(', ')})`);
       }
     } else if (node.quals) {
+      const qualsStr = this.visit(node.quals, context);
       if (this.formatter.isPretty()) {
-        output.push(` ON ${this.visit(node.quals, context)}`);
+        // For complex JOIN conditions, format with proper indentation
+        if (qualsStr.includes('AND') || qualsStr.includes('OR') || qualsStr.length > 50) {
+          if (this.containsMultilineStringLiteral(qualsStr)) {
+            output.push(` ON ${qualsStr}`);
+          } else {
+            output.push(` ON${this.formatter.newline()}${this.formatter.indent(qualsStr)}`);
+          }
+        } else {
+          output.push(` ON ${qualsStr}`);
+        }
       } else {
-        output.push(`ON ${this.visit(node.quals, context)}`);
+        output.push(`ON ${qualsStr}`);
       }
     }