MOV is Apple's homebody: gorgeous on a Mac, awkward everywhere else. It was born in 1991, Apple's QuickTime team, and its real weak spot is traveling: Windows, Android and the web would all rather meet an MP4.
MKV is the format that hoards: video, a dozen audio tracks and every subtitle, all in one box. The Matroska container: it will hold practically any codec ever made. That makes it the right destination when what you need is high-quality rips and archives with multiple audio and subtitle tracks.