I originally posted the manual registry edit solution for enabling PCI-E 3.0 within Windows 7 about a year ago.  Alas, it is near the end of 2013 and I have migrated all of my gaming systems over to Windows 8.1 Pro.  But, what a nasty little surprise I was in for when I discovered that PCI-E 2.0 is enabled by default and not 3.0 on my same exact hardware setup for which I had previously had Windows 7 Ultimate installed.  PCI-E 3.0 worked flawlessly on that operating system build, so it baffled me that Nvidia has yet to enable PCI-E 3.0 be default in their newest R331 series graphics drivers.  To my unhappy surprise, the registry patch Nvidia released last year that automatically enabled PCI-E 3.0 in Windows 7 does NOT work with Windows 8.  So, tonight I tried using the same manual registry edit procedure that I used with Windows 7.  The good news (and what a relief it was) is that is does work for all versions of Windows 8, Windows 8.1, Windows 10, Windows 10 Pro, and the Windows 10 with the Anniversary Update (ugh).  Since the original forum thread that I posted the registry edit steps has been closed, I am reposting the steps for all to use as needed.  So, without further ado, here are the steps for manually editing your Windows registry to enable PCI-E 3.0 on those of you who have Sandy Bridge CPU based systems:
 
These are instructions on how to enable PCI-E 3.0 using the REGEDIT function within the Microsoft Windows operating systems:

Hardware requirements in order for these directions to work properly:
 
1) Motherboard is PCI-E 3.0 hardware certified
 
2) Graphics card (NVidia or AMD) is PCI-E 3.0 hardware certified

NOTE: I highly recommend you ensure the motherboard is updated to the most current BIOS version and that PCI-E 3.0 (GEN 3) is enabled within the motherboard BIOS settings.

>>CAUTION!!<<  Back up your registry before proceeding! This will ensure that you can restore your registry should you enter an invalid value or conduct one of the steps incorrectly.

Step 1: Update your graphics drivers to the latest version (doesn't matter if you use the WHQL or beta version) and restart your computer.

Step 2: Download the latest version of GPU-Z:
http://www.techpowerup.com/downloads/SysInfo/GPU-Z/

Step 3: Run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 2.0 for each card

Step 4: Disable SLI -or- Crossfire (if enabled). If SLI -or- Crossfire are not enabled, skip to Step 5

Step 5: Click on the Windows button (located on the lower left corner of the start bar)

Step 6: In the search index entry window, type in “Regedit” (the Registry Editor window will open)

Step 7: Select the following registry:

HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video

Step 8: Identify the correct registry folders for each of graphics cards you have installed. There will be one associated folder for each card installed. To identify the correct folder for each card, you will need to review the names of each folder within the “HKEY_LOCAL_MACHINE/SYSTEM/ CurrentControlSet/ Control/Video” registry directory. The folder associated with a graphics card will have three or more subfolders (depending on how many PCI-E slots available on the motherboard). The values listed for each subfolder will be 0000, 0001, 0002, 0003, 0004, and Video. Review only the subfolders labeled as "0000". You will know you have selected the correct "0000" subfolder when you see a registry labeled “DriverDesc” with a value that matches the graphics card you have installed. Example, the value in my “DriverDesc” registry value reads “NVIDIA Geforce GTX 1080”.

Step 9: Right click on the folder labeled “0000”. Select “New”, then select “DWORD (32-bit) Value“, then enter “RMPcieLinkSpeed” for the name of the registry.

Step 10: Right click the “RMPcieLinkSpeed” registry you just created, then select “Modify”, then enter “4” as the data value and verify that the “Hexadecimal” option is checked under “Base”, and then select “OK”.

Step 11: Repeat steps 9 and 10 for each graphics card associated folder (named “0000”)

Step 12: Once you have completed creating the RMPcieLinkSpeed registry for each card, close the Registry Editor window and restart your computer.

Step 13: Once your system is back into operating system environment, run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 3.0 for each card.

Step 14: Re-enable SLI -or- Crossfire as needed.

CONGRATULATIONS!! PCI-E 3.0 is now fully enabled!  :D
 
NOTE:  You will need to re-accomplish this entire process each time you update your graphics drivers.  Until Nvidia fixes this issue or you upgrade from your Sandy Bridge CPU, we are stuck with the manual registry edit solution :( 

Doesn't PCIe 3.0 automatically?

after driver 327.23   on my gigabyte z77 board I now have to do this crap to get pcie 3.0 support
 
come on NVIDIA!!

Shakaw
On my windows 8.1 machine, both cards are detected and render tested as PCIe 3 out of the box.
I have always forced gen3 on the slots in BIOS though

This registry hack is only required for Sandy Bridge systems.  Your Haswell system will have PCI-E 3.0 enabled by default.

Did this last night to mine, thanks.