I'm the same as Neil: rip video to .mkv as it is content agnostic (that is, it is a container file you can put anything in - including subtitles and chapters). Sources: BRs, DVDs, off-air TV records (I'm doing this a lot these days), various cameras that have different video formats....
All my CDs are ripped to single file FLACs with CUE sheet support as this is both lossless and means I can get back the original CD if I want/need to and gapless playback is not a problem. I can also pretty simply re-rip the FLAC to .mp3 should I want to put it on a mp3 player (in fact, quicker than I can transfer it to the player). And no, I don't use an iPod because I like to be able to just transfer stuff to the mp3 player without having to sync it.
Basically, apart from the video recode (which I do to reduce storage requirements) everything else is held in the original format from the source material - which means DTS for most BRs, DD/AAC for broadcast and DD for DVDs.. This means should my playback equipment improve, I still have access to the original source data without recourse back to the silver disc/original broadcast.
The beauty of an open system for playback is that if new formats appear (as happened with DTS and AAC in the time I've been streaming video) they can be implemented with an improved codec pack.