Mencoder is free, runs on both Windows and Linux. It is however command line based so you'll have a lot of reading to do before you even get started. Mencoder comes bundled with
Mplayer.
If your converting from a DVD stored on your hard disc (as opposed to a single vob) you could always try
Handbrake or
Xmpeg. I prefer
Dvd::rip on Linux. All three of these support 2-pass encoding. When last I tried IMTOO's DVD ripping software it did not handle two pass conversion very well.