So, on a Win 2008 R2 Std x64, I have 6 (six) gacutil.exe all different (not counting ones in VS folders), in:
This is not the best answer, but I'm noticing an observation. Use the latest version folder, based on whatever you're using for your application being developed for the associated Visual Studio install.
C:\Program Files (x86)\Microsoft SDKs\Windows\{SDK version}\bin\NETFX 4.5.1 Tools\gacutil.exe
When comparing the Control Panel > Programs and Features > "Installed On" date for my Visual Studio installs, I'm seeing many different folders under here. I'm guessing multiple folders got updated during these two installations.
Folders where "gacutil.exe" resides and modified date:
C:\Program Files (x86)\Microsoft SDKs\Windows\
C:\Program Files (x86)\Microsoft SDKs\Windows\v6.0A\ - 3/20/2014
C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\ - 3/20/2014
C:\Program Files (x86)\Microsoft SDKs\Windows\v7.1A\ - 5/15/2015
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.0\ - 3/20/2014
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.0A\ - 5/15/2015
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.1\ - 5/15/2015
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.1A\ - 5/15/2015
Windows Visual Studio Installations with "Installed On" date:
Visual Studio 2012 - 3/20/2014
Visual Studio 2013 - 5/15/2015
To get a comparison of what is in the GAC, I ran this command and diff'ed the files to compare.
cd C:\Program Files (x86)\Microsoft SDKs\Windows\v8.1A\bin\NETFX 4.5.1 Tools\
gacutil /l > c:\v8.1A.gac.txt
Then I changed the folder appropriately for each version.