Nintendo Gamecube USA Missing
From Redump Wiki
(Almost) all USA GameCube games that were sold normally in stores are believed to be dumped. Additional versions may exist (ex. version 1.00 vs. version 1.01). Todo: crossreference with this list for discs / versions that are known to exist.
Possible Game Revisions
Europe has 1.00 and 1.01 dumped, USA probably has a revision too:
Shrek 2 (Player's Choice) Tiger Woods PGA Tour 2004
Unknown if these revisions exist. No 1.00 in redump for these titles:
Batman: Dark Tomorrow Bionicle Heroes Dance Dance Revolution: Mario Mix Disney's Hide & Sneak DreamWorks Madagascar Egg Mania: Eggstreme Madness Game Boy Player Start-Up Disc (Have 1.02 and 1.03) Harry Potter and the Sorcerer's Stone Hot Wheels: World Race Killer 7 (2 Discs) Mario Party 7 Mega Man Anniversary Collection Nickelodeon SpongeBob SquarePants: The Movie Odama Pokémon Box: Ruby & Sapphire Serious Sam: Next Encounter Tetris Worlds Tom Clancy's Splinter Cell: Pandora Tomorrow World Series of Poker
Official Application Discs
Aging Test For Production. try59 (maybe there are other versions?) Memory Card Tool Read Check Program [DL-DOL-022E-JPN] 
Properly dumping unlicensed discs is difficult requires a modified Clean Rip that fills in holes with 0's. Unknown if more versions of Action Replay series exists.
Action Replay 1.08 Action Replay 1.09 Action Replay 1.14a Action Replay 1.14b Action Replay 1.14c Action Replay 1.18  Action Replay Max Freeloader 1.06 Freeloader (Wii compatible)  Max Drive "special bonus disc packed with Power Saves - GameCube game save files"  Ultimate Codes: Metal Gear Solid: The Twin Snakes (Datel. never released?)