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What applications are recommended for encoding existing videos from various sources (ripped DVDs, MKVs, AVIs ...) into a format playable by the new (2010) Apple TV?

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Somebody's gotta make the first obligatory post recommending HandBrake—might as well be me.

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I'm under the assumption that Handbrake only encodes disks, not pre-existing videos. – Jake McGraw Sep 29 '10 at 13:48
As it says at HandBrake 0.9.3: Released! (and also on the front page of their site): " Universal input - HandBrake is no longer limited to DVDs: it will now accept practically any type of video as a source." – Dori Sep 30 '10 at 3:53
@jakemcgraw I encode videos with it every day. I haven't used Handbrake to encode actual discs in close on a year. The source can be any video, and I am using it at the moment to prep about 4000 videos for Apple TV. – BinaryMisfit Sep 30 '10 at 13:47
I would suggest that you use the SVN version of Handbrake to get the latest presets. – fideli Sep 30 '10 at 14:20

The new Apple TV really doesn't really decode individual video codecs - it streams them from local and remote sources. I suspect, though I'm not 100% sure since I don't have mine yet, that if you're interested in streaming to your Apple TV from a local computer, you should convert to the standard formats well supported and playable by iTunes (h.264, quicktime) which will stream over the new(ish) airplay support.

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But, what applications, if any, should I use to convert my existing library? – Jake McGraw Sep 29 '10 at 13:49
My point is that if your existing library is already in iTunes, no need to convert! – Nick Sep 29 '10 at 15:00
Probably wasn't the issue here, but it's possible to install Quicktime Components to extend what Quicktime-using apps like iTunes can play (e.g., FLAC). AFAICT AppleTV can't be similarly extended to support these. So just because someone can play something in iTunes doesn't mean they can play it on AppleTV. – Ken Jul 20 '12 at 23:57

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