Doom 64, for starters. It doesn't seem to get a lot of love around the community from what I've read, and it's actually one of my favorites out of it and the first two. Both the gorgeous new sprites and the level design/architecture, I loved Midway's take on Hell, for example.
Metal Arms: Glitch in the System is another gem, a gen 6 third person shooter. Had some kickin' music, mad weapons and Doom levels of carnage, especially in the later levels. It was actually supposed to get two sequels, but Blizzard swallowed the studio up. The multiplayer was sweet too.
I also loved Mischief Makers on N64, an action-platformer by Treasure. Had some pretty unique gameplay to it.