Lithium II - My favorite DM mod. Very simple, no client side download needed(you'll get it when you connect to a server). Lithium II adds a hook & runes. Sounds simple, but the runes are awesome and make DM a lot of fun!
Weapons Of Destruction - Another DM mod that is fun. Is also server side. Changes the weapons to make them more powerfull. Ex: the machine gun shoots rockets! Craziness.
GXMOD - Gamers Extreme Tournament Mod. Another server side mod that is a must for tournament play. Does not alter DM at all, but rather adds a count down timer, game timer, adds to HUD, advance spectator modes, etc.
3 Team CTF - Great fun at LAN Parties when you have each team in a seperate room or area.
Eraser Bot - Hands down best bot for Quake 2, this one has been around since just after Quake 2 came out, and improved to near perfection since then.
Quake 2 Basketball - Yes it's true! You can play basketball in Quake 2! It even comes with bots to practice against! Fans of both Quake 2 & Basketball will be in heaven.
Q2Tetris - Thats right, a port of Tetris to Quake2!
Capture The Chicken - A funny and cool mod where the object is to steal the chicken from another player. Whoever has the chicken the longest when time runs out wins.
QPong - Not at all like the original Pong, but rather places you on a team trying to get a large ball in the opposing team's goal.
Holy Wars - Standard DM mod where you are a Sinner, and you become a Saint by killing another Saint. You can only score frags if you are a Saint.
Revenge Of Stroggos - An interesting DM mod which allows you to play as different Stroggos!
Gun Slinger - A DM mod that puts you in the old west.
Jail Break - DM Mod, when you kill someone, they go in your team's jail, when you capture their entire team, it's time to execute them!
Other popular mods that I don't care for, or never got into:
Action Quake 2
Rocket Arena 2
Navy Seals
Air Quake 2
Rail Arena
Loki Minions CTF
Brush Surface Attribute Specifications
Quake2 3.20 gamex86.dll source code
Console Commands - A complete list of console commands.
Quake 2 Source Utilities - The WinNT utilities id software used to make Quake 2, other then Microsoft Visual C++ 4.2 of course! This includes id software's level editor QE4 and qbsp3, qvis3, qrad3, etc and their source code.
QERadiant - A freeware recompiled Win32 friendlier version of QE4.
Quake 2 Utils - Everything you need to compile your Quake2 map: qbsp3, qvis3, qrad3.
Wally - A .wal editor. .wal's are Quake2 textures.
Photoshop .wal Plugin - Lets you save images directly to .wal format!
Quake 2 Palette - 5 versions of it.
WorldCraft - A very good Win32 map editor.
Quest - A popular DOS map editor.
Quake2 Done Quick - A run through of the entire game in hard mode in 16.5 minutes!