That's where some of the fancier media server software comes in. They can transcode between formats on the fly when serving up the data. So WMA/FLAC can be served as WAV. MKV can be turned into M2TS.

Pioneer PDP-5020FD, Marantz SR6011
Axiom M5HP, VP160HP, QS8
Sony PS4, surround backs
-Chris