The remaining online Dreamcast games are cross-platform:

Quake III Arena is cross-platform with PC, although obviously only with particular maps. Its online functions via user servers.
StarLancer is cross-platform with PC, the official servers still being up.
4x4 Evolution is cross-platform with PC and Mac, the official servers still being up. The PS2 version is no longer supported.
Sega Swirl is cross-platform with PC via the "play over email" function. I can't imagine anyone actually bothering with it, though.
Phantasy Star Online's private servers are cross-platform between Dreamcast, Gamecube, and PC, though obviously the Dreamcast version is limited compared to the other versions. The Xbox version and PSO Plus don't work.