Oh, the grand tales I could recount of my glory days of online gaming...
Starsiege: Tribes was and is the greatest multiplayer FPS ever. Marathon and Quake were good, but were nothing when compared to the grandeur of Tribes. There were different classes to pick from (well, essentially classes), an interesting arsenal (with weapons that *gasp* took skill to use), a plethora of vehicles, base defenses (turrests and such), jetpacks for everyone, excellent map design, and a huge amount of players on each room (up to 32, I believe). I know that most FPSs have those things today, but Tribes was the franchise that introduced those things.
Half-Life, in all of its wonder, wasn't a terribly interesting multiplayer game on its own. Luckily, the mod community was absolutely huge. The only other games I can think of with such a community are ye olde Doom and Quake. You could find mods with all sorts of themes. There were Tron-themed mods, Western mods, counter-terrorism mods, action movie mods, bullet opera mods, DBZ mods, feudal Japan-themed mods, realistic modern combat mods, and even a racing mod...and those were just some of the multiplayer mods. The mods I spent the most time on were Counter-Strike (from the glorious early days of its final version release), Day of Defeat (the mod that started the whole WWII-craze), Team Fortress Classic (pure gold), and Firearms (spectacular mod that never really became that popular).