OMG I'm not alone! I have the exact same problem!! And it happened all of a sudden. Even my benchmarks are laggy.
I've completely uninstalled and reinstalled all the latest drivers. I've done a system restore. Temps are not a problem, I'm under water cooling. I've monitored task manager and see nothing taking up resources. I also flashed the BIOS and ran everything at stock settings. I also have an additional problem. On a cold reboot and some resets, my system won't post without pushing the reset button (It will just stay on a black screen) I'm at a loss here. Help would be greatly appreciated.
Cpu: Intel i7 3960X Overclocking @ 4.5
MB: EVGA X79 Classified BIOS ver.47
Vid Card: EVGA GTX 680 4GB (2xGPU's) SLI @ GPU Clock 1215/ Memory Clock 3564
Memory: Corsair Dominator GT 32GB @1866
Case: CoolerMaster Cosmos II
Sound Card: Sound Blaster ZxR
PowerSupply: Corsair AX 1200i
Extras: Koolance water cooling setup inclucding cpu and graphic card full cover water blocks. 1x 360 radiator and 1x 240 radiator
Hard Drives: 2x SSD Intel 520 120GB Raid 0 and 3x Samsung HDD 1TB ea. Raid 5
Moniter: 46" Samsung TV
You have to check your core GPU speeds when the lag is happening. There has been an issue where the GPU won't properly clock up to full 3D speeds. For me, it would happen from time to time in Skyrim when going from one indoor location to an outdoor location. The GPU core speed would only be at 405 MHz, rather than the stock 772 MHz for my GTX 580. Restarting the game usually fixed the problem.
After about a week of trouble shooting I found the answer that worked for me. It was a bad stick of memory.
This caused issues like cold boot problems, games being laggy for no reason (when before they played just fine), laggy web surfing, random BSOD's, some applications not displaying correctly (the OK or Apply button with letters cut off), Graphic cards not utilizing full power or performing severely under powered.
All of these issues have been fixed. I hope this helps someone.