Yes, the performance difference between the 9800 XT and the X800XT are quite dramatic, and if you can afford to do so, I'm quite sure that you'd be happy with the upgrade.
There would be little appreciable difference in performance between the AGP version of the card, and a PCIE version of the card, unless of course you had a much more powerful CPU in the PCIE motherboard.
And there's a point.
To more adequately 'future-proof' yourself, you'd need to go a bit beyond that 2.6GHz processor. When PCIE becomes the established standard, as it eventually will, the AGP interface format will have a very limited lifespan left. I highly doubt that processors for Socket 478/AGP motherboards will ever go beyong the 3.4GHz ones which are currently available. I also doubt that you'll see Socket 478/PCIE motherboards.
A jump from 2.6GHz to 3.4GHz isn't really enough of a performance increase to warrant the expense, and as the Radeon 9800 Pro is quite capable of handling any game currently available or slated for release in the near fture, perhaps a wait until the new standard is more widely available and more cheaply obtained would be a wise move?
Food for thought, anyway.
Moved to 'Hardware', by the way