For 360:
Borderlands 2 Vault Hunter's Edition
CoD 4 Limited Edition
CoD World At War Limited Collector's Edition
CoD Modern Warfare 2 Hardened Edition
CoD Black Ops Hardened Edition
CoD Modern Warfare 3 Hardened Edition
CoD Black Ops 2 Hardened Edition
Dead Rising 2 Zombrex Edition
Duke Nukem Balls of Steel Edition
Fable 3 Collector's Edition
Metal Gear Solid HD Collection Limited Edition
Tomb Raider Collector's Edition
For PS3:
Duke Nukem Balls of Steel Edition
Killzone 3 Helghast Edition
(also Infamous and Infamous 2 Special Editions, Resistance 3 Steelbook and Uncharted 3 Special Edition)
For Wii:
Zelda Skyward Sword Limited Edition Pack
The Last Story Limited Edition
Pandora's Tower Limited Edition
Monster Hunter Tri Classic Controller Pack (not that special, but looks nice next to the others
)
Also have an HMV exclusive tin for Pokemon Platinum which isn't really a special version as such, but seems to be rare enough to warrant a mention