I've got a Prometheus and a Mediator in a couple of 4000's, one towered.
Most of the time I prefer my Z3 cards over the PCI ones.
1. If anything goes wrong during boot, the auto-switch lets me see the problem.
2. Using normal video modes with the auto-switch is seamless.
3. It seems more stable.
4. I've only got two drivers to deal with.
I don't get crazy high resolutions or 3D, but to me the experience is more enjoyable.
I've had the Prometheus in the 4000D with the case closed but like others have said, right angle adapters and flexible ribbon card extenders are your friend.
