OK, $800-1000 total for all parts.
Definitely go for a quad core, either AMD or Intel. All of the programs you listed will benefit from that. Phenom II is roughly equivalent to Core2Quad, both in price and performance. i7 will get you more performance, but the platform costs a bit more.
I don't know much about AMD, so somebody else should probably chime in. I chose the fastest PIIX4, and an AM3 motherboard. You could save a few bucks by choosing an AM2+ mobo and DDR2 RAM for similar performance. I just choose AM3 & DDR3 to give a better upgrade path in the future.
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AMD Setup
CPU: Phenom II X4 955 - $210
http://www.newegg.com/Product/...x?Item=N82E16819103674
Mobo: ASUS M4A78T-E (AM3) - $140
http://www.newegg.com/Product/...x?Item=N82E16813131366
DDR3 RAM: G.Skill F3-10666CL8D-4GBHK - 4GB - $65 (I just chose this rather arbitrarily)
http://www.newegg.com/Product/...x?Item=N82E16820231189
AMD Sub-Total = $415
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Intel Setup
CPU: Core2Quad Q9550 - $220
http://www.newegg.com/Product/...x?Item=N82E16819115041
Mobo: Gigabyte GA-EP45-UD3R - $115
http://www.newegg.com/Product/...x?Item=N82E16813128359
DDR2 RAM: G.Skill F2-8500CL5D-4GBPK - 4GB - $50 (I just chose this rather arbitrarily)
http://www.newegg.com/Product/...x?Item=N82E16820231166
Intel Sub-Total = $385
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Common to both Intel & AMD
Hard Drive(s): Western Digital 640GB Black WD6401AALS - $75 x2 = $150
http://www.newegg.com/Product/...x?Item=N82E16822136319
(Note: I recommend 2 because you use one for OS/Apps/scratch drive, the other for storage. If your workflow involves a lot of simultaneous writing/reading to a drive, you may want to pick up a 3rd drive.)
(Note2: the non-Black version WD6401AAKS is $5 cheaper and is very close in performance.)
(Note3: the 1TB Black WD1001FALS is $100. More space, little bit faster)
Case: Antec 300 - $55
http://www.newegg.com/Product/...x?Item=N82E16811129042
PSU: Antec EA650 - $75
http://www.newegg.com/Product/...x?Item=N82E16817371015
Video Card: ATI 4890 - <$200 (or Nvidia GTX260 216 <$180)
many choices available.
Common Sub-Total = $480
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Totals (not including shipping and/or tax)
AMD = $895
Intel = $865
If you're going to be overclocking You should budget an additional $50-75 for a good CPU Cooler.
Don't forget to budget for a backup. a low power green drive in an enclosure at the minimum.
Like I mentioned above, you might be able to get a different mobo/RAM combination for the AMD setup. I just don't know enough about them to give a good recommendation. That would drop the price to probably exactly the same as the Intel option.
If you need to shrink that budget a little, you can get a less powerful video card, somewhere between $100-150. A smaller quality PSU down to maybe around 500w for around $50. And you could just go with one drive if you don't do a lot of heavy disk access. For the CPU on Intel side you could drop down to a Q8200 for around $160, and on the AMD side a PIIX4 940 for about $175 (PIIX4 920 for $150).
If you can expand the budget a little I'd say double the RAM first. Then add more hard drives, possibly in some combination of RAID. Then I'd get a nicer case. All of these would probably still net you less than $1000.
If you have a Microcenter or Fry's near you check for prices there. I know Microcenter has the Q9550 for $170 which is a steal at that price. And the Q8200 is sometimes available for just over $100.