There is a gacutil.exe for each version of the .NET Framework. You need to use the one that is the same as the assembly you wish to un/install.
.NET v1.1:
%windir%\Microsoft.NET\Framework\v1.1.4322\
Visual Studio 2005:
C:\Program Files\Microsoft Visual Studio 8\SDK\v2.0\Bin\
Visual Studio 2008:
C:\Program Files\Microsoft SDKs\Windows\v6.0A\bin