If you're willing to wait for Apple to get AirPlay working consistently on iOS devices (and hopefully on OS X, but that's another story) your problem might be mostly solved. With AirPlay, you'll be able to use apps like YXplayer (although I understand that there's some hard feelings out there about that particular app because of GPL violations) and VLC for iPad to play your media "through" to Apple TV.
Any iOS application that already uses standard media playback components should get free and immediate access to AirPlay add-ons. Unfortunately, as Engadget points out, the unreleased AirPlay is still in its early days and appears to be audio only at this time. Hence, the need for patience as Apple finishes building this new technology so it can start shipping around November.
Still, waiting for AirPlay is probably a lot easier than converting everything, especially if you've already spent a lot of time ripping the DVDs you own into non-iTunes-compatible formats.
As for OS X support, Apple has yet to announce let alone promise a date for AirPlay integration. However, when it does, it's likely that apps like QuickTime X will be able export to Apple TV as well. Add in Perian's power of multi-format playback and you'll be able to bypass iTunes without all that extra work.
If you can't wait for AirPlay solutions to go live, there are any number of terrific video-format converters, rippers, and transcoders out there for OS X. Auntie tends to use Handbrake, an old copy of iSquint, VLC, and ffmpeg but doesn't really have an endorsement for an all-formats solution. Uncle Brett is fond of Evom as well. Maybe her TUAW nieces and nephews can recommend their favorites in the comments.