There are X850 models in AGP as well, but it wouldn't be a huge difference.
PCI-E is THEORETICALLY faster than AGP 8x, but the limit of AGP 8x is not reached with current cards.
PCI-E with SLI (Nvidia cards) or CROSSFIRE (ATI cards) support enables two video cards to be used in tandem, allowing two high end cards to be paired to start with, a high end with the option to pair it later, or a single / pair of midrange cards.
I would go one of two ways, if making the step to PCI-E...
1. Nvidia Nforce 4 chipset, for AMD processor - if going mad for power, a SLI capable motherboard, fitting a single high end (7800 series) card to start with, and a dual core AMD X2 processor.
2. Intel, Intel chipset (dual core support), loaded with an Intel 840 CPU - far cheaper dual core than AMD, but not as powerful.
I wouldnt put a (performance) AMD on anything other than an Nforce chipset, and I would never use an Intel on anything that wasn't an Intel chipset - having found older Intel on Intel setups to be robust, stable and well tuned.
Personally, though I now have Intel with ATI graphics, if I ever build again, I'm going back to AMD with Nvidia graphics - and I'd probably go for the ULI chipset motherboard which supports both AGP and PCI-E - well, if I had an AGP card worth keeping at the time.
I would NEVER go "legacy free" unless certain that running old serial and PS/2 kit on a USB dongle would work in any environment I would wish to run it under.