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Blender
From Quake Wiki
Blender is the free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation. Through user plugins, it supports older game model formats such as Quake & Hexen2's *.MDL, Quake 2's *.MD2, Quake 3's *.MD3, and Quake 4's *.MD5. Blender's website
Add-ons
Here are some addon adding support for the following formats.
.mdl : classic vertex animated format.
- Khreathor's mdl Blender addon based on Bill Currie's outdated quake forge version for Quake / hexen2
.md2 : The mdl format used in quake2.
.md3 : A more precise mdl used in quake3.
.md5 : Used in doom3 & Quake Rerelease.
.iqm : opensource skeletal format.
Tutorials / Help
Fairweather has a YouTube channel series: Modeling for Quake that covers many of the aspects of working with Blender for Quake modeling.