Hmm, Dxf Or 3ds
You should (read: might) be able to import, fiddle with, and then convert those directly to a q3 supported model format in Blender. ase format is the best way to go - take a look at http://wiki.beyondunreal.com/wiki/Blender
for suitable export scripts.
For some pretty decent tutorials on converting a mesh to .ase for q3, you can hit up kat's site at http://www.quake3bits.com/htm/tutorials.htm If you run into trouble, post either here or at quake3world and kat or I should be able to sort you out.
DXF & 3DS Yes
Yah use Blender as DXF and 3DS are ok to use and import into the app now; the latest version has native import support for them.
Getting them out though you'll want to export to ASE as BlackDog suggested, it's much easier to work with if you're not familiar with the process.
What you're going to need to do though, depending on the size of the model, is break it up into smaller sections that'll need repostioning and centering to help with regards to overdraw and such like.
If you check the tools section of my site you'll find all the currently working ASE import and export scripts.