The Prometheus sticks out quite wide on an A3000 with the standard desktop-style Zorro riser. So an average tower probably wouldn't work too well.
Personally, I think it'd be cool to mod out an older server case. They can be found for mega-cheap at trade shows, auctions, etc.
That should give you good airflow, plenty of drive bays, and a solid power supply (you'll need to build an AT or ATX -> Amiga cable, though).
Heck, if you look around a bit, you might be able to find a server case with live SCSI bays such that you could plug that section right into your HD controller. Then you could mount your HDs in the old hot-swap cartridges. (Just don't pull 'em while the Amiga is running!) :-) It could be pretty slick. (though it would be large...)
