I've figured a way to export from milkshape to blender, and then to Quake

You experience it as buggy. Why don't you use a mdl.editor that catches *.md2 files and sends them out to *.mdl?
Sorry for Milkshape, but it lacks this feather. Lots of other extentions, but no quake1.
Here is one:
q2mdlr9b
This one imports and exports mdl and md2 simultaniously.

So now that's a better way to import your q1 models into Milkshape. You say you want to stick with Milkshape. That is your own choice, if you are familiar with it.

Now the other way around. You want the milkshape ms3d file turned into a quake1 mdl file?
First thing I would think of is to export it to a q2 md2 file and import it in the q2mdl editor above. Then export it back to q1 mdl format.

So far your question. There are more quake mdl editors. Misfits is a free model editor and has a lot more import extentions, than the only ms3d of Milkshape.

misfits 

Cool to see people using Milkshape after all these years. 

Thanks for the response, I'll have try exporting to .md2 and then .mdl like you said. Sucks that there's no direct way to go about it but I guess thats what I get for using Milkshape. 

I used to export directly to MDL.

To export it directly to MDL you should use the "Tools->Quake->Compile QC file" option in MilkShape3D. But first, you must create a proper .qc file in the same format used by id Software's MDL compiler.

MilkShape3D is a lot more intuitive to use than Blender, the only part that sucks in it is the texture editor. Too bad MS3D was completely discontinued and the price is too high for me. 

You won't find the q2mdlr9 editor anymore.

If it was on the direct way for q1 models be lucky, because I did much more idiot ways to get them going.
:P 

Hey mankrip, it looks like what you said would work, but I'm still having trouble with the QC. The $skin flag seems like it needs an .lbm file which is some kind of proprietary skin file generated from a .tri file from texmake. Can something similar be done with a milkshape file or a bitmap?
From what I remember, there are license keys from MS3D out there. 

Just use a Windows bitmap.

Here's my qc file for the models in Fightoon:

$modelname newmodeu
// $cd d:\games\quakee~1\testwad\newmdls
$flags 0
$origin 0 0 0
$scale 1
$base base
$skin newmodel.bmp
$frame base
$frame framea01

As you can see, you don't need to be fully explicit about frames. After compiling the MDL, you can rename the frames in qME.

I even used qME to do the texturing, since I couldn't figure out how to create textures in MilkShape3D itself. 

Thanks for the reply mankrip. I've successfully exported an mdl from ms, but the texture co-ordinates don't transfer. I can open the mdl in qMe and move the coords from the top left but then none of these coordinates are marked as seams, which I think is why the mdls won't render correctly in Quake. Everything else seems to be fine from what I can tell. 

Yes, the texturing is the worst part.

In qME, I used the button "Recalculate the skin vertices" to reconstruct the skin vertices from the base frame.

This is why you need a frame named "base" in your qc file. In this frame, the model must be posed exactly as you want it to be seen in qME's uv editor - which means no fancy uv mapping, just the same front + back uv mapping as in vanilla Quake models.

After recalculating the skin vertices, you can delete the base frame or move it to the last position after all other frames.

It's a very awkward process. I don't know if there's a way to make MilkShape3D compile the skins properly, so the whole skinning must be done in qME. 

It seems like I've got it now. "recalculate the skin vertices" was labeled as 'run skinmap wizard' on my copy of qme. It put seams in the .mdl & textures look normal now. And in case anyone else reads this and is having trouble, in the top left pixel of the texture needs to be filled in with the last color in the pallete. Or thats what I did to get it to work anyways. Thanks again mankrip and everyone else who helped, it was majorly useful. 

If you want to investigate further, I suspect MilkShape3D tries to do the whole uv mapping in the same format that Half-Life's models does. This means that maybe inserting HL styled fields for the texture in the qc file and creating the required files may work to compile the uv map.

From what I can see by googling it quickly, it seems that the HL version of the model compiler requires "material" data and related fields in the qc file. 

If I had to guess you're probably right about milkshape using HL style UV mapping. I fiddled around with some HL style qc commands and it looks like milkshape won't accept them when compiling for Quake. When I'm better at programming someday I'll just have to make my own compiler I guess.