Blender SMD Exporter
Exports reference and collision meshes, bones, bone weights, and animations. I do not in any way support the modification of imported SMDs as the importer plugin (not made by me) does not import bones properly.
Currently there's an issue with bone enumeration while animating. It's recommended that you use the plugin download from below, however if you're having a problem with the root bone then you should try the one above. I will be updating this plugin for use with Blender 2.5 soon enough, and will be fixing this issue as well as the majority of any others people have been having. Sorry for the inconvenience.
Download "fixed" plugin (right click > save as)
Installation and Support
Valve Developer Wiki article on Blender
YouTube tutorial (code snippets used here)
Support thread on Facepunch