There are some apps in the Mac App Store that you would only ever find if you happen to be looking in the right place at the right time. Smart Converter, and its younger brother Music Converter, are two such apps.
Smart Converter will convert just about any type of video file format that you throw at it into just about any format. Just drag the video you want to convert into the window and choose what you want to convert it for. Apple TV, iPad, iPhone, Android, Xbox, Windows, PlayStation, you name it. It'll even automatically send Apple formatted videos to iTunes for you. Music Converter works much the same way, doing much the same thing, only for music. Have an AVI file you want on your iPhone? Or a song in FLAC that you want in iTunes? Smart Converter and Music Converter are your new best friends. They may not be the prettiest things in the world, but they get the job done.
And the best part about them both? They're free. Or, at least there's a free version, although it limits you to only being able to convert one file at a time.