Remember that the V3 alpha software is just that: Alpha, and if you're interested in the player being stable and rock-solid, then V2 software with MP3s is still your best bet.

For my money, MP3 is still the best bet even with OGG and FLAC availability, because of the huge amount of available tools to work on the files. Things like taggers, trimmers, organizers and such are plentiful for MP3s, and fairly rare for the other file types. There are things I can do to my MP3 collection with tools like MP3 Tag Studio that I can't do with any other file type.