As for horrible DX9 support on the FX cards, gee whiz, I never noticed the difference between the FX5900 and the 6600GT except for the FPS increase now that you mention it........ am I blind or is just the apps I'm using?

Why would PCI expansion be that much better than an onboard chip? I mean, many onboard solutions are already AGP compliant and use at least 64mb of reasonably fast DDR system ram.

Have you tried maxing out the system ram shared to the onboard video chip in your BIOS? While you are in the bios, you can set your AGP aperature as well, and perhaps the transfer mode for the AGP to 4x if the options exist.

If you have, say, 512mb of RAM and share 128mb, (if thats possible), then your system can only use the remainder of memory not allocated to the onboard video.

Say if you only have 256mb of RAM, and you share 64mb to the onboard video, you are left with a serious shortfall in RAM, and yes, more ram would help.

The only recent PCI card I've seen running in a modern and powerful PC was a GF FX5200 PCI card and it was horribly slow, and my experience in upgrading onboard videoto PCI video has been that it only offers marginal improvement.

The better PCI graphics cards also tend to be expensive by contrast to their AGP and PCIe counterparts, and this brings the financial aspect of "flogging a dead horse" to light.

The reality is that any card you add to that machine is not going to give you great graphics, in fact, they may still disappoint you.

There are two real upgrade options and they both mean a major system overhaul, but there is a big difference in cost.

The first and cheapest is to buy a nForce2 mainboard and a powerful Sempron CPU, unless you already have a powerful socket A CPU you could transfer to the new rig. The same goes for the RAM, if you already have at least PC2700 RAM, then you could transfer that as well.
To  this stuff, you add a shiny new 6600GT video card.

Basically, what I'm saying is that you need a new mainboard with graphics support as well as a new video card. THEN you wil see a dramatic improvement.

Secondly, you could go whole hog and get a socket 939 mainboard, Athlon64 CPU, RAM if required and then a PCIe video card.

Any old ATX case is fine, this is my old junk with a bit of paint on it.

This type of midi tower frame is extrememly common and they are generally of standard type, which means they have all the right stuff in all the right places.

Plenty of room for extra drives and full size mainboards, fan positions/fans  etc.

Your PSU may need to be ATX 2. compatible, which means it has an extra 4 pin power connector to connect to the mainboard. I don't know what you have now, but if the current PSU is suitable, it can be moved, along with everything else, into a nice big ventilated box that's easy to work with.