Although you can technically still upgrade your GPU, you might be better off just waiting until you are ready for a PCI motherboard / system upgrade.
I wouldn't pay the $30 price premium for AGP (just checked AGP vs PCI-E on pricegrabber), which is inferior in virtually every way compared to PCI. It's also a dead-end architecture, so even if you can snag, say, the 3850 AGP, you're just prolonging the inevitable death of your rig.
Better just stick with what you currently have for now, I say. Besides, if you can run the Orange Box at high / very high settings at 1400x900, that doesn't mean more recent games will look like poo on your rig (although they will look like poo compared to a high-end rig, of course!); at worst, recent games should look no worse than the graphics you are experiencing with the Orange Box today.
Games-wise, have you tried "The Ship"? It's available on Steam and all I can say is it's "different" from your average run-and-gun FPS; I've never had to take baths in my shooters before! Since it's based on the Source engine (and available on Steam for USD19.99), running the game should be smooth sailing for your rig.
Also, check out this site for some "Good ol' Games": http://www.gog.com/en/search/sort/genre/shooter
Happy fragging!