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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?

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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.

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I'm sorry to say that the native video player in iOS is quite lacking in features.

Switch to VLC for iOS. You'll be able to play your Handbrake-produced files without problems, switching between multiple subtitles, audio tracks, etc.

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Have you looked at RipIt? It rips DVD's with all of its features. You're essentially creating a disc image with the same data as the DVD. You can play this file in DVD Player. RipIt has a compress feature that compresses the DVD video into an iTunes/iOS friendly format. I am not 100% sure, but I believe subtitles are included in the file. You can check out their website and try the app for free.

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See my edits. I do indeed use RipIt but it doesn't support multiple audio tracks or soft subtitles. – Tim Visher Jul 28 '11 at 12:55

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