Unlike the older 2D games, the 3DS probably isn't powerful enough to emulate the N64 reliably using existing emulator cores (New 3DS should be able to, but I doubt the original could), and configuring a modern controller layout for the N64 is always an issue too.
I recently got a game called Four Sided Fantasy on sale on steam. Quite a short game, and not difficult, but it was a fun puzzle platformer with a unique game mechanic. Definitely would recommend it on sale, although maybe not at full price.