I have been using Handbrake and iDentify and they both work amazingly.
I did download iFlicks, but it wasn't working correctly and iDentify worked immediately. So I have since purchased the app and have used it daily.
The only show it's had trouble with so far is Grey's Anatomy, but i'm not terribly worried about that, since i'll be deleting it once I watch it anyway. I mostly just watch the show, because I have watched it for so long, haha
Thanks so much to all of you who gave suggestions and helped.
Using the Apple TV and iTunes for my movie and TV show collection seems much better than the way I was using it when it was jailbroken. I'm happy with the transition and the change
I also gave one of my extra ATV2's to a friend of mine and suggested the same set of tools to her, so she has been using them as well.