H.264 for Video iPod Conversion
I've been using Videola which has been OK and is free, but the user interface is confusing and it is easy to create invalid iPod Video formats particularly with variable bit rate encoding. It's best to stick to 640Kbps video and 128Kbps audio and you get good results.
Using Videohelp, I found DVD-Guides.com - H.264 FAQ & Basic Conversion Guide.
bq. If you just need to do a simple conversion, I suggest SUPER, a GUI for ffmpeg and mencoder that can use x264 to create an H.264 encoded file. We show how you can do that in the guide below this FAQ. If you want to convert DVD to H.264 the best choice would be "Fairuse Wizard":http://www.fairusewizard.com/. Other free solutions to convert DVD to H.264 are MeGUI and Gordian Knot.
SUPER seems to be the one that these guys like and it looks like it has more control for random video files or use Fairuse if you are backing up a DVD to H.264. It has an aamzing number of parameters though, so is more daunting that Videola.