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Modelling
From Quake Wiki
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 QMLE
.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.