1) To use the wrapper with Project64, for Paper Mario:
a) put the "Glide3x.dll" (the wrapper), into the same place as Project64.exe.
b) pick the Glide64 plugin.
c) in the Glide64 options, it is highly recommended to select "hardware framebuffer emulation". This will fix the speed problems associated with those nasty RAM<>VRAM texture transfers, which are used for some special effects in Paper Mario like:
* the "Tidal wave" effect
* Motion blur etc..
However, you might need to select "read every frame" to have a correct pause screen background (remember that read every frame can be very slow for some games, and it helps greatly to have HWFBE enabled.
But, the problem is, you need a video card that is at least fully compatible with DX9 (as DX9-class cards generally have a OpenGL 1.5/2.0 implementation, which is needed for the functions in the wrapper that enable HWFBE to be usable.)
Oot should work almost 100% perfect with Glide64 and the wrapper.