Some answers, hopefully! :)
OK, so a quick Google search on ProTools and FL Studio show that they are multi-threaded, but, to be perfectly honest, they don't go into a lot of detail. It was literally one line in FL Studios feature list and a few forum posting describing multi-threaded-ness on ProTools. So, I would definitely get a quad, but I think you knew that already. The part I'm debating is AMD/Intel quad. From my research, ProTools seems to work rather nicely with i7's, with a certain bench (Dverbs, if you've heard of it) it gets twice the score than a Q6600.
If I were you, I would go i7. But, realize, you'll need DDR3. Core i7 can ONLY take DDR3, no DDR2 here. For the best performance with i7, we do want triple-channel memory. I'm not fully versed on the performance benefits from double to triple-channel, but the prices are close enough and i7 has a memory controller built for triple-channel, so why go slower? And, like I said, prices are close.
Do you plan to overclock? If so, I would go for one of those cases. But if you aren't, you don't *NEED* the cooling that those cases give and a cheaper case will suffice.
But, here's the rub. The cheapest i7 is $280. An i7 motherboard will run you $200 or more, a few dipping into the high 100's. Memory (6GB, triple channel) will be another $100. If you're counting right, we're at $580 and we haven't even bought the sound card, which sounds pretty important considering the tools you're using.
We can dip down into Intel quad's or AMD's quads, but the i7 may be a bit out of your price range. Both AMD/Intel quads are great. AMD has cheaper motherboards and are a little more overclocking friendly, but Intel's quads are faster per-clock than AMDs. A 3.2GHz AMD (Phenom II 955) is a bit slower than the Q9650 (3.0GHz).
Research your tools a bit, see what other people are using them with. Some tools, unfortunately, are highly biased to one architecture or another. See if there are any anomalies there.
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