Ok, let's take a step forward. Knowing that he is on a Mac Mini, what software would he do to do that?
And knowing that I am using Windows 8, what would I use to do that? Handbrake in both cases or...?
Subler for OSX (as runaway prisoner pointed out)
For Windows, there's a multitude of programs.. but most recently I've had very good results with XMediaRecode.
Select .mkv file
Choose output format (Apple iPad, whatever)
*important* under Video Tab, make sure you select Video Copy
Add Job, Encode
Since it's just copying the video, there is no video encoding done. Essentially it's just taking out the video stream from the .mkv and putting it in an .mp4.
The whole thing should take less than 5-10 seconds.
Notes:
- for simple mkv conversion to mp4
- (if the mkv had multiple audio tracks, you can select which one you want)
- from the looks of it, it seems like the audio has to be re-encoded to aac (no audio copy)
--- this might be necessary if the audio is not "apple compatible", such as ac3 (.mp4 container doesn't officially support ac3 or mp3, so apple playback would throw a fit)
- this will only work if the underlying stream (the raw h264) was already "apple compatible":
--- there are some video files that are ridiculously compressed using very advanced encoding techniques that apple quicktime and stuff might not like. if it doesn't play in itunes, then it won't copy to iphone/ipod/stream to apple tv
--- in this case, you really would have to re-encode the video portion
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Different method: use MKVExtract to extract raw video and audio, then use YAMB to mux back into mp4 container (assuming the video and audio files are already "apple compatible")