• Vincent (1982)
• Frankenweenie (1984)
• Pee-wee's Big Adventure (1985)
• Beetlejuice (1988)
• Batman (1989)
• Edward Scissorhands (1990)
• Batman Returns (1992)
• The Nightmare Before Christmas (1993)
• Cabin Boy (1994) only producer
• Ed Wood (1994)
• James and the Giant Peach (1996) only producer
• Mars Attacks! (1996)
• Sleepy Hollow (1999)
• Planet of the Apes (2001)
• Big Fish (2003)
• Charlie and the Chocolate Factory (2005)
• Corpse Bride (2005)
• Sweeney Todd: The Demon Barber of Fleet Street (2007)
• 9 (2009) only producer
• Alice in Wonderland (2010)
• Dark Shadows (2012)
• Abraham Lincoln: Vampire Hunter (2012) only producer
• Frankenweenie (2012)

Short films

• The Island of Doctor Agor (1971)
• Houdini: The Untold Story (1976)
• Stalk of the Celery Monster (1979)
• Doctor of Doom (1979)
• Luau (1982)

Animator filmography

• The Lord of the Rings (1978) (uncredited)
• Stalk of the Celery Monster (1979)
• The Fox and the Hound (1981) (uncredited)
• Tron (1982) (uncredited)

Cameos and other film work

• Singles (1992)
• Hoffa (1992)
• The Nightmare Before Christmas (deleted scene)
• Men in Black 3 (2012)

Art filmography

• Frankenweenie (1984) (storyboard artist, uncredited)
• The Black Cauldron (1985) (conceptual artist, uncredited)

Internet shorts

• The World of Stainboy (2000)

Television

• Hansel and Gretel (1982) (director)
• The New Alfred Hitchcock Presents – episode The Jar (1986) (director)
• Faerie Tale Theatre – episode Aladdin and His Wonderful Lamp (1986) (director)
• Beetlejuice: The Animated Series (1989–1991) (executive producer)
• Family Dog (1993) (animation designer, executive producer)
• Hollywood Gum – French commercial, director (1997)
• Kung Fu and Mannequin – Timex commercials, director (2001)

Music videos

• "Bones" by The Killers (2006)