FLAC is the audiophile's handshake: CD-perfect sound at roughly half the shelf space. It was born in 2001, Josh Coalson; now kept by the open Xiph.Org Foundation, and its real weak spot is fitting in pockets: lossless is still large: and charming Apple's own apps.
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.