Well, as some have noticed, Nintendo's online store no longer sells the 2-disc GCN Game Cases. So, I thought it might be helpful to contribute a little something back and work toward compiling a list of GCN Games that came in the 2-Disc case. Perhaps this will help someone looking for a replacement case, if they manage to find one of these games cheap.
So, off the top of my head, here's some to look for. If you know of more, please feel free to add and I'll update the OP.
This list regards the US releases only...
1080 Avalanche (early copies with bonus mini-DVD)
Baten Kaitos: Eternal Wings and the Lost Ocean
Baten Kaitos Origins
Enter the Matrix
Freaky Flyers
Goldeneye: Rogue Agent
Killer 7
Legend of Zelda: Wind Waker/Ocarina of Time 2-Disc Set
Lord of the Rings: The Third Age
Metal Gear Solid: Twin Snakes
Metal of Honor: Rising Sun
Metroid Prime/Metroid Prime 2 Demo Disc
Metroid Prime/Zelda: Wind Waker 2-Disc Set
Mario Kart: Double Dash (Special Edition)
Outlaw Golf/Darkened Skye 2-pack
Pac-Man World 2 with Pac-Man Vs. (Player's Choice)
Resident Evil Zero
Resident Evil
Resident Evil 4
Resident Evil Code: Veronica X
Ribbit King
Tales of Symphonia
Teenage Mutant Ninja Turtles 2: Battle Nexus
Teenage Mutant Ninja Turtles 3: Mutant Nightmare
Tiger Woods PGA Tour 2004
Tiger Woods PGA Tour 2005
Tom Clancy's Splinter Cell: Chaos Theory
Tom Clancy's Splinter Cell: Double Agent
Thanks to "Sir Don Komarechka II, esq." of ElectricPickleOnline.com for throwing a few titles at me I forgot.