Modelling

To keep it short: Make models in w/e 3d modeling software, like Blender, 3ds MAX etc. Export to FBX (it supports animations).

Then use Noesis to convert to MDL or other format supported by quake engines, like IQM

Blender

Blender is a free and open source modeling suite that includes tools for modelling, texturing, rigging and animating. Using plugins Blender can export directly into many of the formats supported by various quake engines

FIXME: Write sum tutes ya mooks!

.mdl

classic vertex animated format.

ajmdl_export quakeforge tools

.md3

quake3 mdl

Katsbits import and export scripts, tools and utillities

.md5

doom3 mdl

Katsbits import and export scripts, tools and utillities

.iqm

opensource skeletal format.

iqm devkit