h264 seems to be the new kid on the block. Here is a GUI for a command line encoder you're probably going to end up using (-8

http://www.videohelp.com/tools/MeGUI

Guide to pull your DVD to mkv/h264 file:

http://kitty.110mb.com/dvd2avc/dvd2avc.html

Popcorn Hour, they recommend a bunch of software. Here is the forum link, and the one at the bottom will do DVD→mkv directly:

• http://www.networkedmediatank.com/viewtopic.php?t=3178

AutoMKV - Recommended for BluRay/HD-DVD/DVD → MKV conversions

• (.95c - Stable)
• (.96 BETA - has 'PCH' profile)

Looks like avidemux2 might be the program you want to try.

Russ emailed me a set of instructions on how to encode video for the mst3k stream, so I posted it: MST3k encoding for 128k stream