Although I don't know of any such command-line-driven programs, remember that you can keep windows minimized. Winamp plays pretty much any audio file type. You can set it up for shuffle mode, track mode, track repeat, or repeat mode, pretty much your standard CD-player kind of thing. I don't know if Winamp supports playlists (I never use them). When you want to change songs, click on the minimized window in the task bar (or alt+tab) choose the song you want to play, and minimize it again. I have Winamp constantly running and I almost never see it, even though I haven't minimized it either.
Of course, there are other audio players around - Winamp is the only one I'm aware of. It's free and very flexible.