MKV vs MP4 (M4v)
• more widely used/universal
• can't use dts 5.1 sound (i think, or something like that)
• can "mux" (combine) multiple video files (multiple aspect ratios) / audio files (multiple languanges) / subtitles (multiple languages) / chapters file
• not widely accepted
Mkv vs Mp4
If i have a simple file (say, a "simple" 1080p movie), i'd tend to just use .mp4 because that one file can (most likely) be played with native support in an iphone/ipod/ipad/ps3/itunes/windows 7/etc...
If i had a more complicated file (say, a 1080p movie w/ chapter support, 2ch stereo audio, 5.1 audio, 5.1 audio w/ commentary), then you'd have no choice but to use .mkv (and only be limited to a set amount of players that know how to access each audio file)