The WSPTools now supports 64 bit systems. Actually its only the Cablib.dll that have been build in x64 mode, the .NET code is still x86 but works fine on a Windows Server x64. If you are using the WSPTools source code on a x64 system, you have to use the Cablib.dll x64 version from the binary package.
Happy WSP Building :D
Get the latest release here: http://www.codeplex.com/wspbuilder