I still cannot get certain roms to show up on the rom list:
Banjo-Kazooie (U) [!]
Banjo-Tooie (U) [!]
Super Mario 64 (U) [!]
Wave Race 64 (E) [!]
Wave Race 64 (U) (V1.0) [!]
I have run all of the above through GoodN64, and they all run on PJ64 (apart from Banjo-Tooie, obviously), so they are definitely the right roms. They still refuse to show up on the menu. It's not a huge deal for me, as other versions of the same roms will show (Wave Race 64 (U) (V1.1), or Super Mario 64(E) [!], for example) - so I can still play what I want. It just seems a little strange to me.