Do you have custom background images and boxart/thumbnails enabled? I found that mine froze a lot when I'd move my selection across systems/games too quickly. The workaround for me was to decrease image resolution and navigate the menu slower.
I'm not sure of the possibility of these, but:
-Pilotwings 64
-Donkey Kong 64 with the ability to switch Kongs on the fly
-Paper Mario 64: Skelux's Co-op mod
Pilotwings doesn't run very well, or at all, when injected into wads and wups, and...