Airquake - for reasons previously mentioned. This mod was brilliant and extremely well executed.
Archmage - A lesser known TC that was very influential. He did some very neat stuff, including sly tricks to get things working that weren't meant to. I ended up learning a great deal from his code.
I still shudder at memories of me as a geeky annoying teenager bugging him constantly, and yet he somehow tolerated me and kept replying.
Frikbot - Though rarely played alone as a mod, Frikbot is one of my favorites. It has served as a crucial component of many, many mods I've created, allowing me to actually play my multiplayer mods without a host of quake-playing friends with workable schedules. Multiplayer mods need multiple players, and the Frikbot's incredibly easy plugin steps made it extremely easy to do.
QGren9 (is that the correct name?) - The original predecessor of Wazat mod, my first mod. I don't remember all the details, but I either built off of the mod or began shamelessly pilfering code from it and other mods (eventually making many of my own creations once I had learned how) and eventually ended up with the massive, unsteady conglomerate that was Wazat mod. This sticks in my mind because it's what started it all for me, despite the fact that I'm still unsure of the name. I am a self-taught programmer who got hit start picking around at mods like this and figuring out how they worked, how to duplicate them, and eventually, how to take them to the next step and make something even cooler.
Team Fortress Original - I played this from time to time and it was one of the few mods I enjoyed in online play. Many others required insane numbers of bindings and such, while TF was relatively simple and for the most part you could just hop in and play. The spread of classes gave some nice variety, and let me explore different play styles and find which ones I was in the mood for.
I still need to get into TF2, but I'm not much of a competitive gamer anymore (more cooperative, ala Left 4 Dead). Something about a 9-5 job and 2 hour commute, not having enough time to sharpen my skills, and not having the patience for online trolls and other such problems. Just excuses though...
RenegadeC's TAOV - It's just damn cool that he pulled off a side-scroller and made it really fun!
A variety of weapon and monster mods, including the Airgun, Portal Gun, Raptor monster, and a bunch of stuff off of cdrom.com that I can see in my head but cannot remember the names of.
Snowed and Roids - Really incredible mini-TCs that shook up the boundaries of what could be done.
Prydon Gate - A mega TC that again radically changed the game we were playing, and greatly expanded what was possible.
Fiend Hunter - Though it wasn't terribly playable (no way to beat it or even survive for very long), I was impressed with this mod. Very good, professional feeling weapons, the fiends swarmed and hunted well, and the eggs were just damn cool.
I remember playing one of Dr. Shadowborg's mods and really liking the weapons, enemies, and his use of custents entities (and others) like force fields, transparent particle bridges, etc. I've liked more of Shadow's work too but I just can't remember and connect things together these days.
Custents, for creating lots of cool, practical use stuff.
Nexuiz - Neve mind that I worked on it. It's pretty damn cool what they achieved even before I got involved. I think my addition of the game modes was cool, but they had a fully functioning and popular stand-alone open source game by then. That's quite a dream fulfilled!
Harb's fish mod. You heard me! That thing had me laughing so hard... if you ever find a download link, read the readme first. It's part of the humor.
Quess - just damn cool. I loved the fiend carrying away the dead pieces.
Hurried Descent - Simple concept, perfect execution. A fine example of taking a very light touch to modding to produce great effect, instead of huge, radical changes that don't end up playing well.
A number of maps also influenced me and reside in my memory, like Mr. Fribbles' Electric Fish dm series, Hall of Dread (which I still intend to someday turn into a siege map of some sort, ala Unreal Tournament Assault/Onslaught), and others I simply cannot remember much about beyond brief, cool visions of several rooms, architecture, a really cool ambush, etc. Not very helpful when trying to locate a map. It's like asking a friend about a movie, saying "Hey, do you remember that one movie? With that one guy? The one where he does that funny thing, and... oh I don't remember. Help me out here."
*sigh* The problem for me is I simply cannot remember what the mods I'm thinking of were. Some of them were by the very people in this conversation but I can't remember what they were. I'll add more names as they come to mind.
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Annnd... I of course am very fond of my own mods. But don't tell anyone!
When my computer inevitably explodes and kills me, my cat inherits everything I own. He may be the only one capable of continuing my work.
Full marks to it for accurately keeping the atmosphere of the original game but ramping the brutality, creepiness and fear up several notches. 
