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The PCIe grafic cards are generally faster than the AGP 8x cards. I seem to remember that they made the jump from 130 to 110 nm node width at that time and few of the fastest cards ever made it to AGP. They had to have bridge ICs to run them with the slow AGP bus. AGP simply didn't have the band width the new cards required.

In the end it really depends of your usage, but your best compromise for reliability and performance is probably the dual core 2,3 GHz. I used to have one and found out that it had problems to run H.264 at very high band width without slight hesitations. The quad would not have such issues.
 
Save up and by a Mac Mini Core 2 Duo 9400M..

It'll run circles around G5s, dual or otherwise..

I considered a Mini... But in the end I went Powermac as I could fill it with RAM to my heart's content, as well as PCI-E slots... Being a PC builder, I guess I had an irrational fear for lack of expansion. That and I wanted to do RAID with a Mac in the first place :p And trust me, a G5 with a RAID array would run circles around a mini. But that is, shall we say, expensive.

However, the OP is using single-threaded apps that won't take up more RAM then he can put in the Mini, and since C2D can be considered better then the PowerPC "clock-for-clock", the mini might be for him/her. Furthermore, I am tempted to say WoW will run better on a 2.26GHz C2D with 9400m graphics then my 2.5 970MP with a 7800GT. And I am also pretty sure the OP can get along with external HDs for storage expansion.
 
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