I've been taking another look at video encoding recently, especially the bottom end of the market.
Let me share some conclusions with you:
For desktop encoding SUPER is, well, super. But beware that some versions of this shareware product have been rigged and come with trojans installed. This version seems trustworthy. this product is a bit technical and clunky to use, and does not feature an ftp function so that you can upload your videos, but otherwise it's flexible and covers an extensive list of formats and codecs.
If you're looking to set up a server side encoding system, this can get painfully expensive. the best value product I found on the market was Sothink, although the evergreen Autodesk Cleaner now boasts this capability too. Other solutions, such as those from On2 and Anystream, are considerably more expensive.
If you're looking to get content from DVDs onto iPods and other devices (legally, of course), I can't recommend the weirdly named Cucusoft highly enough. Their products are simple to use with impressive results.
Happy encoding and transcoding!