AFAIK the only rom's missing from the goodn64 database (that are new, not the MIA's) are:
Powerpuff Girls Chemical X-traction (u)
Razor Freestyle Scooter (u)
NFL Blitz Special Edition (u)
Pokemon Stadium 2 (spanish)
all which are found (b/c i have them ;p)
then theres a new Bomberman (j) coming out dec. 20'th but i'm not sure when it will be dumped
and then there are the 4 unreleased ones that are in goodn64 0.999.6:
Bass Racing Ecogear Power Worm Championship (J)
Nushi Zuri 64 - Shiokaze ni Notte (J)
Pro Shinan Mahjong Tsuwamano (J) [!]
Yousuke Ide's Mahjong School (J) [!]
Here's Redbox's mia list
here
that should about do it for the n64 i'd say.. except any demo's, or modified dumps that might come up in the future