What gacutil.exe should I use?

Gacutil.exe is a Windows SDK tool, not a .NET framework tool. You got two versions of the SDK on your machine. You got 6.0A from the VS2008 install, 7.0A from the VS2010 install. You also have a 64-bit operating system so you got the 64-bit tools as well. Which doesn't matter for gacutil.exe, not sure why they include it separately. Probably to keep the Visual Studio Command Prompt working, note that you have separate 32-bit and 64-bit versions of it. Which matters a lot for C++ projects. VS2010 allows targeting both CLR version 4 and CLR version 2 so that's 6 versions total.

What does matter a great deal is that you have two GACs on your machine. The GAC for .NET 4 assemblies is stored in c:\windows\microsoft.net\assembly. For earlier versions it is stored in c:\windows\assembly. You must use the proper version of gacutil.exe to get an assembly into the proper GAC. For an assembly that targets .NET 4, you must use the one in Bin\NETFX 4.0 Tools. And for earlier ones, you must use the one in Bin.

Using it not at all is best, assemblies should have the Copy Local property set on a dev machine. The GAC is a deployment detail, you'll get in trouble when your GAC has an assembly that your user's GAC doesn't have.

Short version: If you have .NET 4.0 installed, use NETFX 4.0 Tools version. Otherwise it doesn't really matter.

Answers to questions:

1. No.
2. Doesn't really matter unless there is no .NET 4.0 installed, in which case you should use NETFX 4.0 Tools version. Not sure if it is possible to have a v7.0 SDK and not have .NET 4.0 installed.
3. No, you can always (and should) use NETFX 4.0 Tools version for all GAC operations.

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\ - 3/20/2014C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\ - 3/20/2014C:\Program Files (x86)\Microsoft SDKs\Windows\v7.1A\ - 5/15/2015C:\Program Files (x86)\Microsoft SDKs\Windows\v8.0\ - 3/20/2014C:\Program Files (x86)\Microsoft SDKs\Windows\v8.0A\ - 5/15/2015C:\Program Files (x86)\Microsoft SDKs\Windows\v8.1\ - 5/15/2015C:\Program Files (x86)\Microsoft SDKs\Windows\v8.1A\ - 5/15/2015

Windows Visual Studio Installations with "Installed On" date:

Visual Studio 2012 - 3/20/2014Visual 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.