As crazy as it sounds, I'll be using the Clip in primarily a fixed position, powered thru a wallwart-USB cable connection, so battery life shouldn't be an issue. We went to Ogg Vorbis for a better sound quality / storage space compromise than basic mp3. I had another person working with me at that time who was quite familiar with the various codec possibilities. (Unfortunately Rockbox wasn't on the table at that time.) Now that I have nearly 3000 sound files, and more coming, I'd hate to have to re-rip everything into something else.
I have a couple of 2G ipods that have been rockboxed. Before that I used a Rio Karma. (I've always thought the Karma sounded a little better, but the ipods are everywhere and cheap.) The RB-2G's sound OK, but took quite a bit of effort to get going and seem more difficult to work with; hence the upgrade to Clips - not to mention cost and size. I guess I wouldn't rule out Rockbox, but unless there are other significant advantages for this app, I probably won't go that direction right now.
I will look into MusicBee. Sounds like a great suggestion! Thanks!