Since gaming is not a priority at all, means SLi and CrossFire are not necessary at all (otherwise X38 could be a recommendation).
By the sound of it, Q6600 is the way to go w/ the cpu intensive task of photo stacking.
As for hard drives, just make a new RAID array from 500GB+ hdds and you should be happy. One of the top Price/performance hdds on the market right now is the WD7500AAKS. Put 2 of those in RAID0 and I'd suspect (shot in the dark here) that w/ your new C2Q/D you'll complete tasks 4x as fast.
I'll go out on another limb here, or at least propose something to you. Switch to Vista 64bit. The biggest thing is if your special stacking program can run w/in a 64bit OS (is the stacker program 16 or 32bit?). The advantage here is when your cpu is in 64bit mode more ALU's or FPU's or something is availible which helps process things faster. W/ a 64bit OS you can also have 4-8GB of RAM availible to you (and DDR2-800 is dirt cheap). I don't know if that extra RAM would help in your line of work though.
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Thank you for not attacking me in your Quote/Bold quote/reply, your question may actually help the OP in making an informed decision. As you seem out to question my posts these days, do you know why I asked the OP if his stacking program is 16 or 32bit?
Here is the article I read that got me to switch to a 64bit OS (Vista of course). When I gave this reply I was going off what I read ealier and didnt recall word for word, but with you here now Idontcare I looked in my history and found it:
http://arstechnica.com/cpu/03q1/x86-64/x86-64-1.html its a good read.
More specifically
http://arstechnica.com/cpu/03q1/x86-64/x86-64-3.html
"When running in 64-bit mode, x86-64 programmers will have access to eight additional GPRs, for a total of 16 GPRs. Furthermore, there are eight new SIMD registers, added for use in SSE/SSE2 code. So the number of GPRs and SIMD registers available to x86-64 programmers will go from eight each to sixteen each."
I guess that doesn't prove too much at face value but after reading that article I was under the impression that a running a processor in 64bit mode can yield a increase in performance. Moving to a 64bit OS is just a suggestion to potentially give the OP more of a performance boost with his new build. He could even install XP Pro 32bit and Vista 64bit to try out the 64bit OS w/o abandoning whats tried and true.