Science Fair Project Encyclopedia

Brer Rabbit, in Disney's Song of the South.
Bugs Bunny
Harvey (actually a pooka) in Harvey
Lola, from Space Jam
The Monster of Caer Bannog from Monty Python and the Holy Grail - a killer rabbit
Oswald the Lucky Rabbit
Rabbit, in the Disney version of A. A. Milne's Winnie the Pooh stories.
Roger Rabbit (originally in the novel Who Censored Roger Rabbit by Gary K. Wolf )
Thumper, in Disney's Bambi
Frank, the 6-foot tall apocalyptic rabbit in Donnie Darko
Characters from Watership Down movie based on the novel (above).
Unnamed (?) pet rabbit in a famous scene from Fatal Attraction.

Rabbits on television

Babs Bunny on Tiny Toon Adventures (NOTE: No relation to fellow rabbit Buster Bunny).
Bean Bunny, in various Muppet series and specials
Benny Rabbit on Sesame Street
Bucky O'Hare in the TV series of the same name based on the graphic novel of the same name
Bugs Bunny
Buster Bunny on Tiny Toon Adventures (NOTE: No relation to fellow rabbit Babs Bunny).
Crusader Rabbit
The Cadbury bunny
The Trix rabbit
Energizer Bunny
The Esquilax (technically a horse) in The Simpsons.
Nesquik bunny
Greg the Bunny
Cartoon Cowboy Gunslinging rabbit - Ricochet Rabbit
Zayats from the Russian cartoon Volk i Zayats (Wolf and Rabbit)

Bun-Bun of Sluggy Freelance, a rabbit with a switchblade.
Bunnie Rabbot of Sonic the Hedgehog (Archie Comics)
Captain Carrot, leader of the "funny-animal" superhero group the Zoo Crew
Coney Dewclaw of Kevin and Kell, a baby rabbit who is a predator.
Kevin Dewclaw of Kevin and Kell
Hoppy the Marvel Bunny, a member of the Shazam family
Danielle Kindle of Kevin and Kell
'Pop' Kindle of Kevin and Kell
Stu and Ed of Faux Pas
Angelique L. of Kevin and Kell (who looks like a rat due to cosmetic surgery)
Joy Satu of Namir Deiter
Kimberly Taylor of Unlike Minerva and You Say It First
Kim Greenwald of The Class Menagerie
Leah Eunomia of Lang Lang
Max of Sam and Max
Skippy of Mynarski Forest
Usagi Yojimbo
In the Erma Felna EDF feature in the comic book Albedo Anthropomorphics, the Independent Lepanian Republic is a political entity of rabbits which is a ruthless enemy motivated by a brutal sense of species supremacy.

Alice in Bloody Roar
Alien rabbits in Space Bunnies Must Die
Cream the Rabbit in Sonic Advance 2 and other Sonic games.
Daisy the rabbit in Doom
Jazz Jackrabbit in Jazz Jackrabbit
Peppy Hare in the Star Fox games
Player characters in the shoot 'em up Rabio Lepus
Rabbit monsters in Final Fantasy XI
Rabite in Seiken Densetsu series
Niccolo in Sword of Mana, a rabbit merchant
Vorpal Bunnies in Quest for Glory IV: Shadows of Darkness
Max in Sam and Max Hit the Road and Sam and Max: Freelance Police (not released)