If you are looking for scripts to help in the encoding process, that wheel has been etched, burned and burned again. If your using any nix, or have access to ffmpeg librarys then you might like these. These are on the sourceforge.net page if your curious. Look for xvidenc, and also h264enc. Also as some other have stated, lots of applications are based on ffmpeg, such as handbrake, and others. In fact most Mac tools for this type of thing probably are based on open source.
If you use those scripts, or any scripts you will soon find that it really depends on the input quality, sometimes you will have to tweak the setting and yes a encode can take up a few hours for good quality.
Also if you hang out on sites such as AVSforum and a few others you will get a good idea of what the people are using and might find something you like. For average folks, some like dvdfab, and you can not forget the king pin, that is almost standard software if your a video type guy. Company is called SlySoft, and make AnyDVD, bunch of other products. Don't forget you can us DD for ISO's and mount under loopback if your on Linux.
Of course we assume that you are following the law, and don't forget about coypright. Sometimes the act of changing formats might be claimed as a violation. ie rip it to hard drive.