If you have more than a few to do, then I would suggest using a ripping program + an encoding program instead of an all-in-one program.
For ripping there are a quite a few pragrams out there, but RipIt and Mac the Ripper seem to be at the top.
For encoding Handbrake is hands down the best program around and has presets for your Apple TV so there's no guesswork.
Here's what I did for my entire dvd collection.....
You can set up RipIt to automatically start ripping a dvd as soon as you insert it, and to eject it as soon as it's done. I also set it up to rip the files to an external HD so all I had to do was keep feeding discs until I had a "batch" of them done. I would do about 12 or so at a time.
Then you can add the rippied dvd diles to Handbrake in it's queue and let it run all night, and depending on your machine they should be done in the morning. This process lets you get throungh a big collection fairly quickly if your not the type to set up the "Automatic DVD Ripping/Encoding/Tagging" scripts as in the sticky thread in the AppleTV section.
Also when you're done encoding let a program like Identify (in the MacApp Store) tag all of your artwork and dvd info, and then put it in iTunes and enjoy.