iVI does this too - all in one app. Pulls all tag info from IMDB (Art work, actors, director, synopsis, genre etc…) then converts an MKV or AVI file you dragged into it, when it's done it imports it into iTunes if you want. If the file you have is already an mp4 or mv4, then you can just tag using iVI, drag into iTunes.
It really is an amazing App and the price is free. Can't beat that.
Before iVI, I did use Handbrake, then went about tagging the file manually looking up the info (OCD about that stuff LOL) - very time consuming. I can drag in a bunch of files into iVI and overnight wakeup to them all done and in iTunes ready to go.
It's one of those apps that really impressed me, much like Air Video which I've been using for years. Just works. And anything that saves me time is great.