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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.
Add-ons
MDL support: Khreathor's qmdl plugin for Quake/Hexen2.
MDL-MD2-MD3 support: Paril's version of Khreathor's qmdl plugin adding Quake 2 & Quake 3 support.
MD5 support: KozGit's addon.
Tutorials / Help
Fairweather has a YouTube channel series: Modeling for Quake that covers many of the aspects of working with Blender for Quake modeling. Modeling for Quake