Thanks to this thread I managed to rip all my GBA library with the 'forcesize' trick I didn't know about at first.

Here a little list of the GBA games with which I needed to force 16mb (All US versions), for science!
-Zelda The Minish Cap
-Sonic Advance 3
-Sonic Battle
-Super Robot Taisen Original Generation
-Super Robot Taisen Original Generation 2
-Golden Sun The Lost Age
-Fire Emblem
-Fire Emblem The Sacred Stones
-Mega Man Zero 4
-Mario & Luigi Superstar Saga
My copy of Zelda OoT (US) did work with the N64 plug-in first shot though, by this I mean before I learned about the forcesize trick. The file is 32Mb and it does seem to work pretty much perfectly with Project64. Am I the only one who's Zelda OoT worked without the trick?