Geez your pulling at your PSU arnt you?

Wish you explained all this in the begining.

I would just build a server.

Yes, but then I'm not using the stock Gateway PSU. It's a 500W modular unit.

I thought I gave all the pertinent info up front (and added more as I learned more). What did I add that was 'missing'?

I worked on a pc some time ago with a lot of HDDs like you have added and a lot of problems occured.Was your mainboard desigened to have this much connected to it?

It has so many issues a server was the best way to go.

You are pulling and nuking your toral resources?

Ok what cooling do you have installed to kep this sytem cooleer with all this hardware installed?

Cooling is all fans, starting with the Antec 900's standard setup (two 120mms on the front panel blowing inward, between the HDDs, a window-mounted 120mm inward over the northbridge and CPU (which has it's own 80mm and duct). The rear of the case has another 120mm pulling hot air out just above the floor-mounted PSU (which does the same with it's own two fans) and lastly, a 200mm on top using the rising warm air against itself by helping it leave out of the top of the case quickly. You can see most of this in my old video of the case with the previous internals...
http://www.youtube.com/watch?v=N1DB9DclaTw

As for resources, it's working fine at the moment, running the 3 IDE, 2 SATA setup. One quirk is that if I hot-swap the SATAs, then reboot, the BIOS gets confused, reordering my boot sequence to a wrong drive. It's easy enough to correct, but to avoid it, I just have to make sure the same SATA is in the rack each time I boot, and since the 250GB is usually there, it's only an issue when I need the 500 in there, which is rare.

What's the latest/greatest freebie SW to get a diagnostic report, to see issues I'm not tripping over yet?

Maybe 'rack' is the wrong term, as I don't mean server rack. It's a 5.25 'trayless' rack for a single SATA HDD.
Newegg.com - Koutech IO-MRA321 Metal 3.5" Black SATA Hot-Swap Mobile Rack - External Enclosures

The rack operates fine now that it's on the MB's #2 SATA port. On #3, it wouldn't work at all and it would disable my PCI card's primary IDE. Now that it's on #2, all work fine (just can't have 3 SATAs in when 3 IDEs are present, it seems).

Jellybean is right, instead of running that many harddrives in your computer, you should probably build a home server, and put those drives in it. one could be built fairly cheaply. As far as i know, there aren't any diag programs that would detect faults on this kind of setup. maybe someone else has heard of something though

I'm clearly clueless on the differences the server would make. We're talking running two boxes with one just managing the HDDs as the user PC demands? What are the benefits? I'm not loving the idea of running essentially two PCs for one user.