I'd say the build value would depend on how cheaply you can find a decent vid card. A used 6800GT would drop in really nicely. The trick will be to limit yourself to inexpensive parts because if you're going to go for a nearly premium build, you're going to waste far more than the price of a new mobo in the long run. As an example, if you wanted to get a top-end AGP card, you'll spend nearly $300 on a 7800GS. But the equivalent PCI-e video card costs only about $200! So you'd actually make back most of that money you'd spend on the new mobo by saving $100 on the vid card.
The same goes for memory, cpu, etc. Stick with lower end parts and you can still build a nice "value" socket 939 agp system. For example, newegg has the A64 X2-4400 for $178, and single core A64-4000 for $79.
Regardless of what you do, don't get a cheap power supply. I've been having random system instability issues and I couldn't track it to any single component or driver, so I gave up troubleshooting and bought a new power supply. My old one was a thermaltake silent purepower which was fairly decent, but it just didn't have the 12v capability I needed. I swapped in a 550w seasonic modular power supply last week (pricy but worth it) and I haven't had a single system glitch since. Plus the modular cables really decluttered the inside of my case, making it much easier to work on.
