Yes, apparently there are still some bugs lurking - for example, Tetrisphere will blow up a little ways into the title screen intro. RB suspects that the RDP is trashing memory, but I have an optional #define for enabling bounds-checking on RDP memory writes and I am not aware of anything that currently trips it. If someone is willing to put in the effort of running MESS until the game crashes with bounds checking turned on (RDP_RANGE_CHECK in src/mame/video/n64.h) and find me an actual repro case, I'll be glad to look at it.
Quite frankly, I would be absolutely elated if it turned out that the frequent random crashes of either MESS or the emulated N64 were tracked down to simple memory corruption by the RDP, because that would mean a whole lot of my worst-case assumptions as to the causes of these issues are completely invalid, so I would much rather be incorrect in this case.