I see for Mac they have something called Subler. But I don't see anything for Windows or Linux. I know for Windows and Linux there is MKVMergeGUI but I don't see anything that can do similar into an M4V or MP4 container to use with iTunes/iPad.
		
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	The default multiplexers for the MP4 container are GPAC MP4Box and L-SMASH. Chances are good that an MP4Box from the "GPAC Nightlies" may be able to read from MKVs and multiplex to MP4 if the content is compatible and supported; if you don't like the Command Line Interface, then e.g. MeGUI should be able to help you (maybe extracting elementary streams before multiplexing). 
 
 The container is officially named "MP4". The filename extension ".m4v" also relates to MPEG-4 Video, but may be more suitable for elementary MPEG-4 (A)SP video streams (as created by e.g. DivX, Xvid) without container, especially without audio; but it is sometimes (mis-) used without much care.
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