WEBM is video the way browsers like it: open, royalty-free and built to stream. It was born in 2010, Google, out of its VP8 acquisition, and its real weak spot is life outside the browser: editors, TVs and Apple devices get picky.
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.