I just have my Music files, my Video files, my Photo's etc, in well organised folders, I click on the file I wish to view/play and the "player" I have assigned to that type of media fires up and plays it for me.
That's what I like and it feels a very clean, fresh, easy and open way of doing things.
I do agree with that, and that's what I do with my media files. But this in no way conflicts with using iTunes to sync with my iDevices. iTunes doesnt get in the way of how I organize my media files, and when I want to sync media to my iDecixes, I just drag them into iTunes, and from there, they sync to my devices. And I love smart playlists in iTunes, they really help further subdivide my media into various groupings that *I* fully control.