I am trying to compile a list of all current gen (PS2 / Cube / Xbox) games which have had a limited edition, or a packaging variant (Such as a store exclusive cardboard sleeve), or simply games which have had a choice of coming with a peripheral... Or, just games that are a little bit on the special side...
Mainly PAL versions, although I have included some notable American versions as well (In red)
So far I have managed to think of:
PS2
Red Faction II ~ LE Cardboard sleeve for early pressings
Dragon Ball Z Budokai III ~ LE Cardboard sleeve for early pressings
King Of Fighters: Maximum Impact ~ Cardboard sleeve
Devil May Cry III ~ LE Cardboard sleeve for GAME
Metal Gear Solid III: Snake Eater ~ Metal Edition
Tony Hawk Underground II ~ Box set with T shirt
Unlimited SaGa ~ Gatefold cardboard case
Monster's Inc. ~ LE Cardboard sleeve for early pressings
Silent Hill II ~ Gatefold cardboard case
Ico Collector's Edition ~ Gatefold cardboard case & art cards
Ico Promotional Collector's Edition ~ Cardboard box containing candle and discs
Medal Of Honor: Rising Sun ~ Metal "Ammo" tin case (GAME exclusive)
Grand Theft Auto Double Pack ~ Cardboard case containing GTA III & GTA: Vice City
The Getaway ~ 1,000,000 Limited Edition (All silver cover)
Transformers ~ LE Cardboard sleeve for early pressings
Time Crisis II ~ Box set with Namco G-Con 2 gun
Time Crisis III ~ Box set with Namco G-Con 2 gun
Ninja Assault ~ Box set with Namco G-Con 2 gun
Sega Superstars ~ Box set with EyeToy camera
EyeToy: Play ~ Box set with EyeToy camera
EyeToy: Kinetic ~ Box set with EyeToy camera
Final Fantasy XI (NTSC) ~ With official PlayStation 2 hard drive
Growlanser Generations (NTSC) ~ With watch and other goodies
Ace Combat IV ~ With arcade flight stick
Xbox
Halo II Collector's Edition ~ Metal tin case
Doom III Collector's Edition ~ Metal tin case
Unreal Championship II ~ Metal tin case
Jade Empire Limited Edition ~ Different cover plus extra content in game
Steel Battalion ~ 40 Button controller
Steel Battalion: Line Of Contact ~ 40 Button controller
Grand Theft Auto Double Pack ~ Cardboard case containing GTA III & GTA: Vice City
Dead Or Alive: Ultimate ~ Cardboard sleeve (GameStation exclusive)
GameCube
Donkey Konga ~ Box set with bongos
Donkey Kong: Jungle Beats ~ Box set with bongos
Donkey Konga II ~ Box set with bongos
Final Fantasy Crystal Chronicles ~ Box set with GameCube / GBA link cable
Zelda: Four Swords Adventures ~ Box set with GameCube / GBA link cable
Mario Party VI ~ Box set with microphone
Mario Kart DD ~ Console pack-in version with bonus disc containing Zelda:Collector's Edition
Pokemon Colosseum ~ Console pack-in version with bonus disc containing Pokemon Box
Zelda: Wind Waker ~ Console pack-in version with bonus disc containing Ocarina Of Time & OOT Master Quest
Resident Evil IV ~ GameStation exclusive cardboard sleeve
Resident Evil IV (NTSC) ~ GameStop exclusive LE tin case
There are other PS2 gun games which come with the G-Con 2, but I can't remember them at the moment. Same goes for the PS2 EyeToy
I will update the list above as people submit information. Pictures would also be appreciated with each new submission.