How can I rip a DVD so that it has multiple audio tracks and subtitles available when synced with my iPad? I'm in the process of ripping my DVD collection to disk for backup, syncing with my iPad, and protecting from my toddlers.

I'd like to have the commentary (if available) and subtitles with the video file, but I do not want the subtitles burned in.

I can't figure out how to make any of the programs I usually do this with work with the iPad. RipIt provides that beautiful .dvdmedia file from which I can simply watch the DVD in DVD Player.app but it's compress feature doesn't bring over anything but the default audio track and it doesn't deal with subtitles. HandBrake provides the option of Burning in the subtitles, which is not what I want, but when I don't burn in the subtitles, the iPad seems to be unable to deal with them, even though I believe QuickTime X does know what to do. Of course, VLC or any other reasonably powerful video player can display them just fine.

Short of encoding them twice, is there a way to get what I want?
You could check out subler, it's a great .mp4 swiss army knife, and supports soft subtitles. I've used it with success with my Apple TV 2, and it work without issue, although I haven't tried on my iPad yet.