Excellent detailed points keenart - learned a lot from your post.

One thing i noticed on my 2 year old Intel D915GAG that you might watch out for:

Intel located the 16x PCI Express connector (which i must use) directly under the power supply conditioning / motherboard chipset and microprocessor sections of the mobo - the parts most sensitive to heat. Modern display cards put out a lot of heat and many (like my new BDG GeForce 7950 GT OC 256) dump that heat directly into your case, rather than venting it out through their adapter brackets.

In my mid-tower case the heat from the display card rises only a couple of inches before dumping into the processor fan - which then distributes it to this vunerable area. Intel warns against supplying air to the processor fan that's over 38 degrees C.

I had to add an extra fan with my display card and at times things do get hot. My Intel P-4 model will slow down to avoid overheating, but does not have additional protection against overheating, if that slow down is not enough (more expensive P-4s have a 2nd level of heat damage prevention).

The point of all this is:
1.It's a lot better if your mobo has the PCI Express connectors near the opposite edge of the mobo from the processor area.

2. Display cards that vent their heat outside the case are cool in more ways than one.

3. You can learn a lot by reading the microprocessor manufacture's technical spec sheets online.

I'm designing my next system at this time and expect to get a heatpipe type Zalman cpu cooler:
http://www.zalmanusa.com/ , even though my new Intel Core2 -Duo won't have the extreme heat proplems of a P4.