007 - GoldenEye (USA): Freezes when loading into a level, or sometimes when going to the main menu. MESS crashes shortly after with a DRC error about a label not existing.
Banjo-Kazooie (USA): Renders the first frame and then freezes.
Banjo-Tooie (USA): Doesn't boot.
Clay Fighter 63 1/3: Freezes on the first frame with an error to the effect of "START_NEXT_TASK: RSP not yielded!"
Conker's Bad Fur Day (USA): Doesn't boot.
Gex 3 - Deep Cover Gecko (USA): Doesn't boot.
Mario Kart 64 (USA): Freezes when going into the Options menu, changing the audio type to Headphones, and then backing out.
Shin Nihon Pro Wrestling Toukon Road - Brave Spirits (Japan): Doesn't boot.
Shin Nihon Pro Wrestling Toukon Road 2 - The Next Generation (Japan): Freezes at the last screen of the intro.
Stunt Racer 64 (USA): Doesn't boot.
MESS crashes in 64-bit
Castlevania (USA): Crashes when going in-game.
Castlevania - Legacy of Darkness (USA): Crashes after its (very good-looking at hi-res!) in-game intro.
Donkey Kong 64 (USA): Crashes MESS after a very glitchy intro.
Indiana Jones and the Infernal Machine (USA): Crashes MESS after a very glitchy main menu. Also has a really odd issue on the LucasArts logo where all of the letters render in one place rather than separately.
Jet Force Gemini (USA): Crashes on startup.
The Legend of Zelda - Ocarina of Time (USA): Crashes on startup.
Rocket - Robot On Wheels (USA): Crashes after legal screens.
Sim City 2000 (Japan): Crashes on startup.
Super Smash Bros. (USA): Crashes on startup.
Super Mario 64 (USA): Black poly-storm for a few frames originating behind the castle front door after getting briefed on the camera controls by Lakitu, then crashes.
Tetrisphere (USA): Crashed after finishing the second level.
Not Working for weird reasons
Command & Conquer (USA): Doesn't recognize that any controllers are plugged in.
Working more or less fine, possibly with video bugs
Bust-A-Move 2 (USA)
Doubutsu no Mori (Japan) (note, I haven't tested this extensively because I do not speak Japanese, but I have verified that the RTC support is working as when I tested it yesterday it said it was 8:10PM on 2/14)