I've been going over and over this for a couple days now and I can't figure it out.  Here's my issue.  I've got 2 9800 gtx in SLI and can't seem to yeild any performance benifits out of them.  In 3dmark06 my score in 12000 with 1 or both 2 running.  Seems too low for one card to be honest.  In Crysis I do see minor benefit in fps when doing in game counts but the looped time demo there is a small drop actually.  I'll post this which I posted in another forum if you guys wouldn't mind reading it for me.
 
First I did a benchrun with SLI again  
For 3dmark I got a whopping 11803...ouch  
sm2.0 - 4377  
sm3.0 - 5783  
cpu- 3366  
 
Obviously that sucks big time for 2 9800 in SLI.  
 
I then took out one card and did another run.  
The score was 11325  
sm2.0 - 4500  
sm3.0 - 5209  
cpu- 3285  
 
I then put the card in to PCI-E slot three and it booted up fine but told me that if I'm not running SLI to put it back into slot one. So I did cause I figure it knew better than me and didn't seem to wanted to do anything else anyway. Seemed normal though.  
 
I swapped that card out for it's handsome twin and he put out an A for effort score of....forgot my drumsticks....  
-11215  
sm2.0 - 4437  
sm3.0 - 5169  
cpu- 3265  
 
So as you can see these two cards pretty much tied for last place out of a 2 man sprint.  
 
I then tried my Crysis benchmark. And played the opening sequences in SLI and with each card individually.  
 
SLI did give me a small boost in certain areas. For the Assault Harbour scene in 1680x 1050 all setting on high no AA it gave me a 10-15 fps boost in the opening scene where the guys are sitting around chatting about how cool the suit is and in general gave me a few extra boosts or 5-10 frames here and there with many scene pushing virtually the same count.  
 
I then did the opening scene of the game and was getting 50 to 60+ fps at the same res and detail level but with 4xAA turned on. Essentially getting AA for free from what I was getting before. On the Assault run I essentially free 4xAA over the single card scores.  
 
So the SLI is making a difference just not as much as I'd expect considering how low the score with one card is to begin with.  
 
I'm thinking I'm bottlenecked by the q6600 at stock perhaps.  
 
Other interesting notes.  
 
-3dmark refuses to acknowledge my 2 cards  
-crysis benchmark heading shows MGPU. It recognizes both cards.  
-Nvidia control panel recognized both cards but tells me I have 512 meg of video memory. Maybe it won't combined the total for both cards.  
-SLI visual indicators often look bored. Bars go from full length to maximum shrinkage like Castanza just getting out of a cold pool.  
-I redid a 3dmark run with the cards rearranged and got 12097 (total), 4368 (sm2), 6205 (sm3), 3269 (cpu)  
 
 
My system is
q6600
xfx 780i SLI motherboard
2 9800gtx
4GB OCZ DDR2 800
PC P&C 750w PSU
Window Vista Ultimate 64bit
 
and I just got the newest driver for my cards.

Hmm that's interesting to say the least.  I would've though you could get 13000 from one 9800GTX...
 
I know my Q6600 @ 3.2Ghz and my 8800GT with a slight OC gets around 11,800 so something is up with whats going on in your setup.  I know my OC'd CPU helps but 3dmark is based more on GPUs and not CPUs.
 
Check your bios settings to make sure you have full bandwidth going through both PCI-E slots.
 
Maybe try a slight OC on your Q6600 and see if it helps improve your score.  I can't imagine a Q6600 being a bottleneck but stranger things have happened.

I can not tell you whats wrong, but even for 1 GTX that 3Dmark score is low, with my old E2160 @ 3.2ghz my 8800GTS 512 got 11707 after being ran immediately after installing the card and the driver with 0 tweaks, upgraded to 3110 and with both @ stock it got 12387.

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Intel E3110(3.2ghz)/GA-P35-DS3L/4gigs DDR2-800/MSI 8800GTS 512 OC/2xSeagate 320 WD 120/Ultra X2 Connect 550/22" Compaq P1220

The Q6600 could be a bottleneck @ stock speeds, so yes an OC would definitely alleviate/show it. I've noticed my SM2 and SM3/HDR scores go up with each higher OC i do on my cpu. which tells me @ stock speeds my 3110 is bottlenecking my GTS

 
Mine @ Stock    678/972(gpu)                 Yours
3DMark Score   12387                   3DMark Score  12097
SM 2.0 Score  5894                      SM 2.0 Score     4368
SM 3.0 Score  5620                      SM 3.0 Score     6205
CPU Score  2768                          CPU Score       3269

@ 3.6ghz @ 748/1000(GPU)
SM2 6478
SM3 5986
CPU  3312
Total 13761

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Intel E3110(3.2ghz)/GA-P35-DS3L/4gigs DDR2-800/MSI 8800GTS 512 OC/2xSeagate 320 WD 120/Ultra X2 Connect 550/22" Compaq P1220

 
I looked through my bios but couldn't find the option to alter my PCI E slot speed.  Are you familiar with the XFX 780i type bios.  Even my manual makes no mention of it.  BTW my CPU score was by far the lowest in the test at ussually just around 3200 points if that's any indication of anything.

Those benchmarks are what I would expect from a single stock 9800gtx, and a Q6600, not overclocked. Perhaps a little on the low side, but in the ballpark. There is something wrong with your setup somewhere when you go to SLI, Its not your q6600.  
Unless it is not being detected correctly by the BIOS?.......but still, when going to SLI your score should show much more improvement over 1 card than it is doing now.

Your SLI board will have dual 16X PCI-E channels so you don't need to set anything in the bios to enable.  At stock speeds for a Q6600 which is the same chip I have, should score a little bit more than that but depending on your tweaks that may be about right.
 
Make sure all 4 cores are enabled in your bios.  Than make sure your SLI is set to enable in the Nvidia control panel because I don't think it is.  If it is, you can also custom add it 3Dmark06 and force SLI just to make sure.  There is also a Nvidia tweak I believe its coolbits available at guru3d downloads will let you turn on the SLI monitor so you can visually "SEE" if your SLI is working in games.  Big green semi transparent load balancing bar appears on the left side of your screen, showing the SLI usage.
 
With a similar setup I get 18084 in 3DMark06 with dual 8800GTX Oc'ed, 9800GTX's are over rated.

My cards are installed in pci e ports 1 and 3.  I tested both port and got an image in both cards and in both ports.  Device manager detects both cards.  Nvidia Control panel detects both cards. Crysis benchmark detects MGPU setting.  My SLI is enable in control panel, bridge is firmly in place.  I don't know what else to check for to see if my sli is enabled.  All signs point to yes.  Could it be Vista?? I'm thinking of RMAing for   9800gx2.  Save myself the sli hassle.  Not that it ussually is.....

Wow surprising I just did a search and compare on a Stock Q6600 and a 9800GTX  
11218 3DMarks
SM 2.0 Score  4209
SM 3.0 Score  5273
CPU Score   3443
 
Your CPU score is little lower, nothing much if you had anything other than your AV running while benching(Teamspeak/MSN would lower my cpu score by 1-200 points) Drivers can make scores lower too. especially the new beta thats for 3DMark Vantage.

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Intel E3110(3.2ghz)/GA-P35-DS3L/4gigs DDR2-800/MSI 8800GTS 512 OC/2xSeagate 320 WD 120/Ultra X2 Connect 550/22" Compaq P1220

Visual indicator show SLI working but the bars expand and contract wildly.  Often look idle.

Goose your cpu... Lets see what she can do !!!!

Make sure your cards are running at the speeds they are meant to be running at using a program like rivatuner.

 
The only time I have seen them do that is when either 3Dmark06 benchmark is initializing and the cards are settling themselves or when a game preview video is starting up, than they will bounce for a bit but once your game or benchmark begin, the load balance should be steady only with slight variations in and out as the load changes within the scene.  This tells me there is something wrong with your SLI hook up. (note they should be green almost from top to bottom from the center out with slight fluctuations on the top and bottom from the center when under full SLI, your are just not working)
 
You might try to reload your drivers because your SLI indicators should not expand and contract wildly once in game or in the benchmark.  There will be variances but not extreme.  There is also the possibility one of your cards is defective but I would try a driver reload first. The load balance is cool to look at and will show you which games use SLI more than others.
 
SLI is not that big a deal and you have done all the right things.

Id say 2.4ghz Q6600 is definately a bottleneck for 2 of those cards.  A fast  dual core would be a significant improvement.  Although I dont believe thats your whole problem.  You definately have something amiss somewhere.  Do you show 4 separate core graphs under control panel performance?

I gotta put my 2 cents in here, you are so right. The 9800's are bit of a disappointment.
 
 

Your cpu score is a little low but your SM scores are very low for a 9800GTX especially the SM 2.0 score.  I am able to get that with a 8800GTS 640.   Sounds like driver issues/conflicts.  Remove, clean and reinstall new drivers or roll back to an older set.  I don't have a 780 board so I can't help you there.

Hrm, I've got a Q6600 on a 780i board myself and a single 9800GTX.  Is it even worth running that card in SLI with that processor?

Yeah I seriously doubt that processor at stock speeds can keep up with 2 GTX's.  He'd be better of with a fast dual core.

Yes it is bottlenecking.
 
I do not have geforce cards. I have 3870x2 cards, and the higher I go on my processor, the more shader performance I get with my quad.
 
it is safe to say that there currently is no CPU on the market that will not bottleneck quad gpus, unless of course you are using liquid nitrogen or phase change at ridiculous clock speeds.