Navagon: Overall, I'd say it's in better shape than UT3.
I wouldn't be a bit surprised to learn that UT2K
3 is in better shape than UT3. I just reinstalled UT3 and the situation is dismal as hell. Every server has bots on it. The populated servers seem to be pubstomp fests but I only bothered playing on a few of them before uninstalling again for the third or fourth time.
What's happened with UT2K4 seems to be a common side effect plaguing games with strong communities. One game variant, usually the favorite, reaches a sort of critical mass where the best servers are focused on it and even advertise the fact with their names. More maps get made for that game type, and the maps available get tested and sorted more rigorously. If the variant wasn't superior to begin with, it eventually becomes superior due to the wealth of good material and the enthusiasm of the people playing.
Of course the down side is if you don't like Onslaught mode you can't really play UT2K4.
Not GOG but no longer Steam-only and uses UT2K4's engine:
Killing Floor. It still attaches itself to Steam but you can get it on disc now for $20. It's entirely a coop game, and unlike Left 4 Deadcraft there's not a "correct" way to approach every encounter, so it's actually fun & unpredictable and the mood stays light.
I didn't see
Giants: Citizen Kabuto or
Fallout Tactics mentioned. Neither has what many people would call "good" multiplayer, but it's because Giants is imbalanced and Tactics is awkward. Also no one ever plays them, but if you have some friends who will follow you into hell for a few hours they might be worth a try. Fallout Tactics is widely despised (albeit mostly by the incurably pissed off Fallout community) but Giants is a wonderful single player game and the balance issues shouldn't matter if you're playing with friends. (I haven't done this in years, so be sure it's still even possible. It might not be.)
Not GOG, but free and a classic:
SubSpace, aka Continuum now that it's player-run. Simple top-down space fights in mazes with casual competition and a focus on teamwork. It's been a long time since I played, but different game variants are alive and I think the leagues are still going.