Q9450 reaches 3.6-3.8GHz with a little effort and good cooling.
Q6600 reaches 4.0GHz with a bit less effort and better cooling if you are lucky.
Neither do that on SLI capable chipsets unless you really know what you are doing and get lucky.
In current games dualcore is better. Age of Conan, Supreme Commander, Lost planet and games yet to come will be better at using a quadcore and thus a quadcore is better for the future.
Your post for a system around $2000 caught my eye. I just ordered my parts for my first build and thats what I ended up spending, at least for now. I probably should have asked around for some opinions but instead just read alot of articles and reviews of products at newegg.com. I'll have to let you know how it goes when I complete the build. I started with an Antec P182 case, DFI LP LT X48-T2R Inter mobo, PC Power & Cooling S75QB 750W power supply,Q9300 cpu, EVGA 512-P3-N801 8800GT 512mb video card, Corsair XMS@ DHX 4GB DDR2 800 4-4-4-12 WD 150GB Raptor 10000 RPM and a WD 750GB SATA hdd's. 2 Samsung SH203-N DVD burners and a Samsung 22" 22ms DVI LCD monitor. MS Vista Ultimate SP1 64 -bit OS. Total $2010, all from Newegg. I couldn't handle buying one part here and one there.
2x150GB Raptor RAID0 Boot drive (~$340)
This doesn't really fit into your budget, since you plan to have a gaming machine but you can try and see how much money remains for graphics.
2x500GB RAID1 backupdrive (size 500GB, redundant) ($180)
2x640GB RAID1 backupdrive (size 640GB, redundant) ($200)
2x750GB RAID1 backupdrive (size 750GB, redundant) ($260)
Only you know how much space you need but if your data is important go with a redundant backupdrive.
EDIT a quick sum:
Option 1: Q9450: $360, 790i $310, 2GB DDR3 $150 : ~$820
Option 2: Q9450: $360, 780i $240, 4GB DDR2 $120 : ~$720
Option 3: harddrives ~$540 (2x150GB + 2x640GB)
Option 4: harddrives ~$430 (1x150GB + 2x750GB)
Option 5: harddrives ~$200 (2x640GB, no RAID)
PSU (750W or above): ~$130 (Corsair, PC Power & Cooling are my top picks)
CASE (Cooler Master): RC-690 ~$110 with shipping
Total without graphic cards:
Option 1 + 3 : ~$1600 leaving ~$400 for graphics (maybe for 1x GTX 280)
Option 2 + 3 : ~$1500 leaving ~$500 for graphics (good for 2x 8800GTS)
Option 1 + 4 : ~$1500
Option 2 + 4 : ~$1400
Option 1 + 5 : ~$1250
Option 2 + 5 : ~$1150