Ubuntu is a community favorite, but I'd check in with the matterhorn mailing list and/or IRC channel to see what folks there would recommend.

Epiphan also makes hardware capture devices, one of which is built specifically to feed the content to Matterhorn servers. http://www.epiphan.com/products/other-applications/matterhorn/

The 3rd party tools are those that don't run in the JVM. These are not bundled with Matterhorn mostly due to licensing incompatibilities -- GPL in particular. They are all open source (ffmpeg, mediainfo, tesseract). Because compiling ffmpeg under windows is not trivial, windows support has come and gone in Matterhorn, and has always been somewhat experimental. I don't know where windows support is at the moment. Most people wind up simply running a linux VM if they can't part with their windows environments.