Hi there flavin,
I can understand your pain. Choosing an AGP Or PCI Express path is one decision I'm also facing in my next upgrade.
Well, to set things straight - without a doubt, the future belongs to the new PCI Express interface. However, the technology is still too new to judge when exactly this future will be upon us; in other words, when PCI Express will become a "must-have". So far, only motherboards using Intel chipsets offer PCI Express at all, although the competition supporting AMD is set to go.
Where 3D performance is concerned,
PCI Express offers at best minimal advantages over AGP models. If you're looking to upgrade your graphics card - you won't be making a mistake if you pick up an AGP model. This is assuming that your system is reasonably powerful and up-to-date.
However, in your situation, since the potential upgrade includes a new motherboard and a CPU,
it's worth taking a look at PCI Express. Keep an eye on the price tag, though, as PCI Express systems on the whole aren't significantly faster than their AGP counterparts at the moment. In the end, it's up to the individual to decide how much an investment into the future is worth to them.
Some background on the graphics processors out there. For NVIDIA, there is the NV43. NV43 is NVIDIA's first "pure" PCI Express graphics processor, especially developed for the new PCI Express bus. In contrast, the GeForce 6800 and the older GeForce PCX GPUs are native AGP chips that NVIDIA makes PCI Express-capable by means of a translator: the so-called HSI bridge chip. For the AGP variations of the GeForce 6600, NVIDIA goes in the opposite direction, by having the bridge chip make the GeForce 6600 GPU AGP-compatible.
Which should you buy, you ask? The advantages of the new PCI Express bus over the AGP are currently more theoretical than real, but without a doubt the future belongs to the newer interface. The higher transfer speed and the ability to send and receive data simultaneously -AGP is only able to go one way at a time - are clear advantages for future applications and new games.
Up until now, however, the industry has failed to provide the practical proof of all these advantages. At least in games - the main application of a 3D consumer graphics card - no advantages can be found at present for PCI Express graphics cards compared to AGP versions.
Adapting a computer to PCI Express is not cheap by any means. In addition to a new motherboard, most of the time you also need a new CPU, cooler, memory modules and potentially even a new power supply.
Since the advantages of PCI Express are minimal, purchase of a new AGP graphics card is the most cost-effective way of improving performance on an existing computer for most gamers, assuming the PC's computing power has been kept up to current standards. Switching to PCI Express makes sense only when the PC is outdated and dragging, and it's time for a general overhaul.
By the way, there's more information about PCI Express in the following post I made:
https://www.techspot.com/vb/topic38629.html
I hope this helps. Let me know if you've any more queries.