MKV is the format that hoards: video, a dozen audio tracks and every subtitle, all in one box. It was born in 2002, the open-source Matroska project, and its real weak spot is playing on TVs, iPhones and editors that never learned to open the box.
FLAC is the audiophile's handshake: CD-perfect sound at roughly half the shelf space. Free Lossless Audio Codec: think ZIP for sound: it decompresses back to the exact original. That makes it the right destination when what you need is archiving music with zero quality loss and a genuine size saving.