The Q6600 is still about $200.00 on Newegg, though it's no longer a top-of-the-line quad core. The E8400 is a 3.0ghz dual core and is down to $180.00 on Newegg -- perfectly adequate for most games since they aren't really coding for multiple cores yet.
Q6600 (oem):
http://www.newegg.com/Product/Product.a ... 6819115018
E8400:
http://www.newegg.com/Product/Product.a ... 6819115037
If you can get an OEM version at a discount it might be worth spending the money to get a good aftermarket heat sink, like the Xigmatek S1283 or S1284, or the OCZ Vendetta 2, which is afaik the best heatsink on the market for anything approximating a reasonable price currently. The Xigmatek S1283 is actually slightly cooler than the S1284 but lacks the fancy LED light fan. I would also look at the Xigmatek bolt-on kit instead of the standard push-pins, though if you aren't going to be moving the computer much the push-pins are probably fine.
Xigmatek S1283:
http://www.newegg.com/Product/ProductLi ... e=XIGMATEK
S1283 bolt-on mount:
http://www.newegg.com/Product/Product.a ... 6835233019
Xigmatek S1284:
http://www.newegg.com/Product/Product.a ... 6835233017
Bolt-on mount:
http://www.newegg.com/Product/Product.a ... 6835233020
OCZ Vendetta 2:
http://www.newegg.com/Product/Product.a ... 6835202007
The better heatsinks may not be necessary, particularly if you aren't overclocking. I just considered mine (the Xigmatek S1283) an investment.
Also, check out the ATI 4850 graphics card. It's gotten rave reviews and is less than $200.00 while handily beating Nvidia's offerings at the same price range. I don't know enough about the different manufacturers to make a specific recommendation, but the Gigabyte 4850 currently has a $30.00 rebate, pushing the price down to $159.99 -- which is damned hard to beat. The 4870 is about a hundred bucks more but is better than Nvidia's GTX260, which is quite a bit more expensive still.
http://www.newegg.com/Product/ProductLi ... 000+series
For RAM, I'd avoid the DDR3 and look for DDR2. OCZ or Crucial are my preferred brands, and I bought 4 gigabytes of OCZ DDR2 for a little over a hundred dollars 6 months ago. Look for an Intel chipset motherboard, either Gigabyte, Asus, or Intel brands. I wouldn't bother getting one that supports DDR2 and DDR3 memory, and I personally wouldn't worry too much about a built-in wireless modem (seems silly to have on a desktop to me!).
In terms of power supplies, I'd suggest something from Thermaltake (never had one but heard good things) or PC Power & Cooling. I've heard from a few different people that Antec's latest power supplies are lower quality than their earlier ones. On the other hand, OCZ apparently has pretty good powersupplies as well. I've also been told Silverstone is really good, but the only one I've ever bought fried my mobo, graphics card, and one of my two sticks of RAM. Might've been an incompetent user error though.
500 watts would probably be more than enough for you, but if you want a 700 watt one to give some room to expand it wouldn't be much more money. Might want to try for a modular PSU so you can detach unused cables and reduce clutter in the case -- I wish I had.
Speaking of cases, I'm quite pleased with my Antec 900, and it's fairly cheap right now since the updated (much larger) 1200 is out. But shop around, since I don't know how much room you have to play with.
You really shouldn't have any trouble building a very good system right now for under $1000.00. You won't be able to play Crysis on all Very High graphics settings, though.