Well i know all these, but you still haven't answered my question. People seem to discredit older machines just because they're old. I've seen some geekbench numbers here, so I guess I'll share some info because it all seems false.
The 3.0ghz quads on my machine give me approx. 11500 to 11900 on 64bit geekbench. Mind you, they are overclocked to 3.6 now, but since it is software overclock I can't test it. Both cpu and ram went up from 1333 to 1600 mhz. I bet you it's more than 13000. Also, I've read tons of articles a while back that geekbench doesn't do very well with paired cpus, which would usually lead to 10-15% less than their actual score. Also, I'd love to see a mini working at 80% and up cpu usage for more than 10 minutes and *not* go on fire or slow down. How could one possibly compare a laptop sized computer with a quality built workstation is beyond me.
About the limitations, yes, it's true. But that's just Apple wanting to make money, what if you don't even bother with OSX altogether? This machine is still of a much higher quality built than your typical plastic PC and that won't change no matter how many new cpu sockets, PCIs, DDRs they make. Btw, PCI 1.0 doesn't really limit you. PCI 3 cards, well that's another story. My point is, people still don't realise just how good the hardware still is, even if its old.
Lastly, i read 'iPod' not 'iPad' so yeah it makes more sense now lol.
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Um, I'm not discrediting older machines, I am just stating what is better for the value for about the same amount of money.
You don't have to tell me about old computers, I have a 2008 8 core Mac Pro and it's a solid machine 
If the OP got a 2008 Mac Pro to trade with an iPad (even a quad core) I wouldn't even be against it, but the OP wants to trade for a 2006 Quad Core, which uses a slow FSB, based on the Core Duo technologies (that is about 8 years old in tech years). Also who knows about the longevity, it might have issues in the future.
The reason I stated this is that if the OP wants to get a 2006 Mac Pro, he would be better off with a Mac Mini for about the same amount of money (also he could look at the Refurb deals and save money) and at the same time he would be saving space and future proofing himself as he could sell the Mac Mini and get a new Mac Pro when it comes out.
The Mac Pro is a fantastic machine, especially the ones after 2008. Point was, for such a big machine (2006) the OP will not be gaining speed performance...but if he just wants a big beautiful box that is slower than a current Mac Mini, he's welcome to buy it.