I'm in the same boat, I also just made my first Quake models. I found it helped that I had mapping experience, because in both cases, you build wireframe meshes of some sort and apply skin/textures to them.

I use QME, which can be downloaded from quakeone.com among other places; it comes with a pretty good manual which is an enlightening read.

http://www.quakeone.com/index.php?ind=downloads&op=category_view&cat_id=8

For skins I use Wally and Paint Shop Pro 4.12, which is an older shareware program (whose trial phase never expires...)

I found it helpful to set the grid size in qme to 2 or 4 units, instead of 0.1. Just read the whole qme manual.

There is also a tutorial by Preach from Quake Expo 06, which is here:

http://www.quakeexpo.com/booth.php?id=32&page=79

Also use google to look around for tutorials etc. 

I've been working on a little project to force me to learn some C++. The program takes an md3 file and a pcx skin, and outputs a mdl file. This would be a good way of skipping the bit of the tutorial which involves messing around with quark. Right now the program works, but it's pretty inflexible. For example, it combines the skins from all the components of the md3 by overlaying them onto the same skin.

It also runs on the command line, so you have to type things in each time you want to convert something. I'd like to give it a proper windows GUI interface, but that's a whole lot of extra learning I haven't got my head round yet. If anyone thinks they'd find it useful it it's current state, give a yell. 

It's a python script run from within Maya that writes out an extended form of .qc that contains actual mesh definitions, coupled with a modified modelgen.exe that reads that mesh data (and .bmp files instead of .lbm). It works perfectly and I have one or two new monsters working in-game already, and they turned out pretty nicely. Doing all the modelling and animating in Maya makes everything so much easier I changed my plans on new monsters in Lunsp2 from "one" to "a bunch" just because the turnaround is so quick.

It is of course not perfect, still in a guts-hanging-out garage-inventor kind of a state, and the documentation exists entirely in my head, and I was going to post it once I'd polished up the rough edges and made it safe for public consumption, but if you have/wanted to use/are willing to try Maya I suppose I could upload something tonight when I get home. Plus, if you're familiar with scripting in your 3d package of choice you could always use just the changed modelgen.exe and write the extended .qc files yourself from Max or Blender or whatever heathen satanist 3d package you use. 

Bloody hell, that would probably get me back into quake modding actually.

unfortunately i'm in the middle of a crunch at work right now, and will be for some time :(

Bollocks >:{ 

I use Max, never got around to figuring out Maya joints.

I'm mostly just hacking up the Q1 monsters ATM, but the heavier stuff will be starting soon. 

Maya > Quake sounds good!

I have no interest in modelling or animating characters, but it'd be nice to be able to make/export basic props from Maya and use them in Quake (I'm assuming it's easy to add custom models using Quoth). 

Yeah, we added that in the latest version, use a "classname" of "mapobject_custom" and model field set to the desired path and model. Spawnflag 1 makes it a static entity, and if you set mangle then that will be used in place of angles - to make odd rotations easier. 

i'm playing around with making props for a map i'm working on but having to skin them the 'quake' way instead of doing it all in 3ds is incredibly annoying. :( 

you can kind of plan around it. I've modelled all my characters thus far with the modelgen projection in mind and gotten pretty good results, without any unsealed edges either. The main thing to remember is, don't have any faces that are parallel to the front - make your legs and heads diamonds or hexes in cross section so that when you do the roadkill you can pull those verts out a bit and pancake the guy to get more even pixel density on those faces that slope away from the z axis.

It helps that next to the existing monsters anything looks good. :) 

it's not that it's hard to do, but that you can efficiently unwrap a model. and that in turn means you can get as much resolution out of the skin as you could. 

to unwrap the UV's the Quake way with Blender. Line the camera evenly with the front face choose an unwrap mode called project from view for the front selection. Invert selection you have the back face, then you can spread it out as you see fit. Blender pretty much emulates Maya methods so that might translate over, or might not. 

The converter I've got for MD3 to MDL preserves the existing UV map on the MD3. It turns out that MD3 models do just duplicate the vertices in the same way that it's necessary to do for quake 1 models. So you can map the skin in as efficient a way as you desire.