This is just a list of some of the best or most useful ones I've seen. I'm lazy though so there are a lot of good sites which aren't on here.
For a more complete set of links, visit enemy-territory.startkabel.nl. This is the best place to go for finding stuff related to ET. There's also a good RTCW portal. Both sites are updated regularly with the newest links to useful websites or news articles.
Wolfmap: awesome ET-site with good news
section + lots of downloads related to ET, RTCW and ETQW. Excellent map collection.
Splatterladder: Et-Rankings, map- and clan database. German and french sections available.
Planetwolfenstein: great forum + guides for newbies
RTCWFiles.com: ton of great downloads,
probably thousands of files here
ET International Resource
Site: great forums + downloads of maps and mods
enemyterritory-stuff: Largest map collection for ET I'm aware of. Successor of 'new-etmaps.de'
RtCW.jolt.co.uk: Very neat site with good tips for RtCW and ET, e. g. how to set up a server for Enemy Territory. Almost complete cvar library.
Et-Scene.de German ET-Community site.
rtcwmap.de German ET-Community site.
enemyterritory.fr French site dealing with all aspects of ET.
Wildstar's Maps Nice map collection
Only4Noob: Very interesting ET-site. Great info on scripting, especially usage of ACSII-code in ET
Antman: scripts-collection, etpro related stuff
Punkbuster: Anti-cheat protection used in ET. Go here for variable-descriptions and manual updates.
ET Pro:
the main ET competition mod, also popular on pubs
Shrub mod: not longer supported... similar are ETPub and Jaymod
ETPub: similar to ShrubET
Jaymod: similar to ShrubET
True Combat: Elite: Enemy Territory goes Counter Strike...
NoQuarter Mod: another popular pub-mod with new weapons, etc.
Server Browsers:
Let you view/join servers, find out where your friend is playing, etc.
Kquery: very good, for free, but not too easy to use. Discontinued.
Pathfinder: also for free, but old program (2001 :() with not so many functions
Game Spy Arcade: Basic version with ads
XQF: server browser for Linux.
Xfire: Free, but you need to register.
GamePulse: Supports only RtCW and ET, in the free version you can only save 5 favorite servers
Qtracker
Other
ET
Minimizer: program for minimizing Enemy Territory (you can use O'Neill's alternative minimizer as well)
Spawntimer ET: Since the Heron spawntimer is forbidden in many leagues, Rude Force created an alternative :p
ET Personal
Progress Indicator: program for viewing various stats info
QVM: Quake video maker,
great for making AVI's
YAWn: tool to detect if people are who they say
they are
Fritz Bot: Another place to download bots...
Omni-Bot: Other Bots...
Just Pub: ET-Comics
ET in Real Life: 2 guys planting mines, calling airstrikes, etc, in their backyard :)
Wolfenstein Flash Movies: Based on RtCW, but is good for ET as well. VERY decent training movies with subjects like this: "The player with the Flame Thrower should always stand in front."