The software I described in the tutorial I wrote up not too long ago has been updated by the author.
From Jacob Klint:
I am the author of the autompeg4 program, and I ran across this guide recently. I’m happy to see others are getting use out of the program!
I wanted to let you know that I just released a brand-new version of autompeg4. It has been totally revamped – it now has a nice GUI, a new name (”MpegALot”), much improved multithreaded batch encoding features, and so on. It still retains a command-line mode though for automated batch encodes as you describe here (although the settings file format has changed so old settings files will not work, sorry for the inconvenience!)
You can download the new program here:
Looks like he has really put a lot of thought an effort into making this an all in one solution, plus it looks like he has included all of the supplementary downloads in his zip file so it can be a one-stop open source solution. Nice. Check out the description here.
For those interested in the automated solution, another piece of software highlighted on lifehacker a couple times is ipodifier, which basically runs in the background, monitoring folders for new videos. When they show up, it automatically converts and syncs them with itunes. Check out the write-up here.