Today - no not really. There aren't any programs or games that take advantage of AGP's enhancements. When this will change - who knows... When I got my latest video card I went with the AGP version (since they were the exact same price) just in case something comes along to take advantage of the AGP.
So, no there really isn't any difference right now in terms of software that is out there... Another reason you might think of AGP is to keep that PCI slot free or something else (NIC, soundcard, etc, etc, etc) since AGP is only for video (at least as far as I know...)
Hope this helps,
Paul