NTSC:
Resident Evil 4 Special Edition
- ESRB.M - Jan 11, 2005 - 013388990467 - only 48,000 made
Tom Clancy's Splinter Cell Chaos Theory Limited Collector's Edition
- ESRB.M - Mar 29, 2005
Arguable:
The Legend of Zelda Collector's Edition
- ESRB.E - Nov 24, 2003 - 045496961480
-Only version made available, not sold in stores though... actually somewhat rare
Star Wars Rogue Squadron 3 Limited Edition Preview Disc
-it was a demo disc but actually labled as a "limited edition" and came with bonus content including a classic arcade game...
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PAL:
The Legend of Zelda The Wind Waker Limited Edition
The Legend of Zelda The Wind Waker Limited Edition (Slipcover Edition)
-HMV Exclusive
Mario Kart Double Dash (Slipcover Edition)
-HMV Exclusive
Mario Kart Double Dash - 2 disc console pack-in
The initial console release of Double Dash had a 2 disc pack-in, where the second disc featured the Zelda: Collector's Edition compilation disc. Subsequent releases of the console bundle would just have a standard one disc NFRS version of the game
Pokémon Colosseum - 2 disc console pack-in
The console bundle for Pokémon Colosseum had a 2 disc pack-in, where the second disc featured the very sought after Pokémon Box utility. Pokémon Box itself was never released for retail, and was only available as a very limited disc from Club Nintendo, or as part of this bundle pack-in
Resident Evil 4 Limited Edition (Gamestation Console Bundle)
-includes a special slip cover for the game and a bonus disc
Arguable:
The Legend of Zelda Collector's Edition
-Only version made available, not sold in stores though...
Final Fantasy Crystal Chronicles
-saw it listed as a limited edition, it looked like a bundle box with a cable included, it's different than the us release but it's not clear if it was actually a limited edition or just a bundle.
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NTSC-J:
Biohazard Collector's Box
- 5 Biohazard (0, 1, 2, 3 and Code Veronica Complete) titles for GameCube in one box (8 discs total)
- Includes Wesker's Report 1 & 2
- Comes with 2 free Memory Cards
- Packed into one box covering the "Umbrella Corp. Emblem"
Phantasy Star Online Trilogy Limited Edition
- Includes Phantasy Star Online 1&2 Plus
- Includes Phantasy Star Online III: C.A.R.D Revolution
- Includes special paper box to hold both games together
Please post up if you know of others or know details about any of the above