- Hunter Hunted (asymmetric multiplayer platformer-shooter with vs. and co-op modes)
- Perfect Dark (FPS with lots of multiplayer modes, including co-op campaign, campaign versus mode[!], and of course endlessly configurable plain ol' arena versus, including highly-configurable bots—the closest I've seen something come to this is Call of Duty: Black Ops 2, of all games, but it still wasn't that close. Most elements/modes exist somewhere, but rarely in one package. The way difficulty levels didn't just make the enemies bullet sponges and better shots [though it did also do that] but also changed objectives and sometimes starting location, was also excellent and isn't as common as I wish it were)
- Return Fire (vehicle-based CTF multiplayer, with elaborate pre-built defensive base structures for both sides—this game's not quite all there, but make it more than 2 player and add a little base-building and it'd be amazing)
- Battletanx (Actually a little similar to Return Fire, now that I think about it, but with a lot more of a traditional multiplayer-shooter feel, different camera perspective, and the vehicles are all kinds of tanks. AFAIK nothing like this or Return Fire has been released since the N64/Playstation era)
- Dominus (The single genre it's closest to is probably tower defense, but it's got a whole lot more going on than most of those)
Also, edutainment disappoints me these days. Drill-type games (as in, drilling math problems) seem to have gotten much better, but sheer knowledge games (Explorers of the New World, Microsoft's Dinosaurs) seem to have all but disappeared, aside from adult-targeted trivia games, which don't have a learning focus and aren't very good at teaching you things. The Trail series (yeah, it's still around, by why aren't there similarly-clever and well-made games for 1,000 other historical situations, too?). I actually think this category would get a lot better, fast, if we had decent, accessible multi-media authoring tools for the web. The closest thing we had was Flash, and it's gone.