I intend to do a speedrun on Project 64 1.6 and was wondering, which skips and tricks do not work on emulator? Plus: Is there anything special I need to be aware of, when I run this game on emulator?

If your ROM is US-NTSC 1.0, you can do every skip and trick in the current route on emulator. JP and PAL versions cannot do many of the tricks but that's a difference in game version rather than console vs. emu.

Only thing that comes to mind that you should be aware of is killing the motorcycle skeletons at the bottom of castle center on emu. That is the likeliest place for the game to crash, so test it out and see what happens.