First off I just wanted to make mention that:

Xonotic
http://www.desura.com/games/xonotic

and

Red Eclipse
http://www.desura.com/games/red-eclipse

Are free on Desura.

The Desura client is also free and only requires a valid email and user name to sign up.

Both games have a lot going for them and Xonotic is actually turning into a fulled fledged shooter like Unreal 2004.

However, I mostly play:

Star Wars Battlefront II
Section 8 Prejudice (6 to 10 normally online)
Unreal 2004 (tons of people online)
Wolfenstein ET (tons of people online)
Quake Wars ET (10 to 20 normally online)
&
Battlefield 2142 (tons of people online)

I'm hoping the top two freebees really start to take off, it would be a shame to see all that effort go to waste and Xonotic comes with a level editor so that you can contribute your own maps.

Apparently Xonotic only comes with a template for levels, you'll need NetRadiant:

http://www.icculus.org/netradiant/files/

Does W:ET still have a thriving community? I really want to jump back into the fray. I love that game. I'd reinstall QW:ET too (which I prefer over W:ET), but support for it is mostly dead, and I'm tired of the same maps over and over again.

I don't have a favourite online shooter atm. Quake 3 CPMA still holds a special place in my heart, but the Asian community is dead in the water thanks to lack of support from id (no Q3A sales, relatively expensive to acquire) and lack of pure CPMA servers. As far as shooters in general are concerned, I'm still waiting for a multiplayer shooter with the level of tactical realism in Red Orchestra 2, minus the suckage of shoehorned vehicular combat.

sounds silly but i still enjoy a good game of UT3 every now and then... or runtfest style invasion maps on UT2k4

There are quite a few people playing Wolfenstein and Quake Wars is still active as well. The best way to check on how populated servers are is to check GameTracker http://www.gametracker.com/
which lists the servers and the number of people using them.

With Quake Wars, however, you're going to have to use the Punk Buster Key Generator that they made for Wolfenstein (which no longer needs it) found here
http://etkey.org/
and Punk Buster Legacy files found here
http://forums.warchestgames.com/showthread.php/31245-Punk-Buster-Legacy-Files-Including-Quake-Wars-question?s=baab4d615c1b4f43a00e4130a01ab0ea Those games still have a lot of online players. Tournament '99 does too.

Red Orchestra 2
Killing Floor
TF2
and Tribes: Ascend is quite good too.

I play Super Monday Night Combat (free on Steam if you care). Hunting frags isn't always the best way to play because it's a team game; situational awareness is more important than a good KD ratio. That said, I have been in some truly atrocious randomly-generated teams, but most of the time it's alright.

Used to play Urban Terror quite a bit until the cheating problem started becoming endemic and using hacks started becoming almost obligatory.

Unreal Tournament tends to have the most civil people in the public servers, CoD 4 isn't bad but filled with overly experienced people against whom it's no fun for an average player to compete.

And I've had paid TF2 in my Steam account now for what must be going on four years and I've NEVER played it.

Counter Strike
Counter Strike Source
Team Fortress 2

Day of defeat. I have only 150 hours played in this, but this are the best online hours I've ever had :P

I'm not a big online shooter person, but I do have a soft spot for TF2. It is fun almost no matter the teams. Payday the heist is also pretty good.