Boy, this forum is a fun one.
Interesting issue, AGP vs PCI-e. And what makes it more interesting is the price point of ~$250.
$250/6months = >$40/month just on hardware to play video games. I know my perspective on this, but does that make financial sense to you?
I think the right answer to this problem is to, as others have said, "ride the wave" a little longer - not because I think you need to wait for new technology or anything, mind you. You just need more money.
If you had come to this forum and been like, "I have $600 and need better graphics!" it would be a no-brainer PCI-e. This PCI-e mumbo jumbo is silly. The interface is faster than it needs to be already. Don't bother waiting on that.
As others have mentioned, AGP is dead. That's correct (even though I still use a GeForce2MX in my old Barton 2500+ comp). However, I dunno what the rest of your build looks like, but if it is as some have speculated (168 pin RAM, IDE HD, pre-ATX 2.0 standard, pre-AM2 slot), it doesn't make a great deal of sense to try to upgrade with just $250, as that excludes a lot of important things, like 240 pin RAM or a new PSU, etc.
If you're not limited by these factors (which I'm almost certain you are, since you don't have an AM2 chip), then no question, upgrade to PCI-e.
If you do have those limitations, it may make a little more sense to buy a better AGP care (but not a lot more sense).
But the best answer is to wait until you have a few more dollars to spend, and just upgrade the whole thing. Nice processor, nice motherboard, and good graphics. And, provided you get one of the up-to-date chip slots (AM2 or LGA775), you should be able to upgrade again on the motherboard you buy and do more piecemeal stuff.
Of course, you need to weigh the options to consider what's best, but as long as you're getting >30fps on your fav. games, suck it up for another month or two and then pick out the best system for what you need.
Good luck.