Season 1: 2004-2005
- The Bat in the Belfry
- Traction
- Call of the Cobblepot
- The Man Who Would Be Bat
- The Big Chill
- The Cat and the Bat
- The Big Heat
- Q&A
- The Big Dummy
- Topsy Turvey
- Bird of Prey
- The Rubberface of Comedy, Part One
- The Clayface of Tragedy, Part Two
Season 2: 2005
- The Bat, The Cat, and the Very Ugly
- Riddled
- JTV
- Swamped
- Pets
- Meltdown
- The Butler Did It
- Fire and Ice
- Ragdolls to Riches
- Strange Minds
- Grundy's Night (aka Soloman Grundy)
- The Laughing Bat
- Night and the City
Season 3: 2005-2006
- Batgirl Begins, Part 1
- Batgirl Begins, Part 2
- A Fistful of Felt
- A Dark Knight to Remember
- RPM
- Cash for Toys
- Brawn
- The Laughing Cats
- Fleurs du Mal
- The Apprentice
- Thunder
- The Icy Depths
- Gotham's Ultimate Criminal Mastermind
Season 4: 2006-2007
- A Matter of Family
- Team Penguin
- Clayfaces
- The Everywhere Man
- Strange new World
- The Breakout
- Artifacts
- Two of a Kind
- Seconds
- Riddler's Revenge
- Rumors
- The Joining, Part One
- The Joining, Part Two
Season 5: 2007-2008
- The Batman/Superman Story, Part One
- The Batman/Superman Story, Part Two
- Vertigo
- White Heat
- A Mirror Darkly
- The Joker Express
- Ring Toss
- The Metal Face of Comedy
- Attack of the Terrible Trio
- The End of the Batman
- What Goes Up...
- Lost Heroes, Part One
- Lost Heroes, Part Two