Are there any relatively accurate N64 emulators with debugging functionality?
I did a search for you and found this
(which is apparently based on the emulator Daedalus). Nemu64
apparently has a debugger as well, though the version listed there (and The Emulator Zone) is as old as 2003.
There is also a debugger project
that from what I gather may be designed for real hardware, but I don't know what point in development it's at.
Hope that helps.
I remember that IIMarckus worked on analyzing Pokémon Stadium so he may likely be of help.
Edit: I tried running Pokémon Stadium on the first emulator and it said "Warning! Unhandled savegame type: FlashRam.", "Error! Exception :Writing to rom" and refused to load, so that may not work.
Edit 2: Project64 apparently
has debugger support.