why are you locally using gacutil.exe?
To include external assemblies in your SharePoint project, for example lets take the Ninject.dll, you just add the assembly as reference to your project as you would do in any other CLR project.
To ensure that the Ninject.dll is included in your WSP you have to open the Package Configuration - just open the "Package" node in your SharePoint project and dbl. click the given entry. Scroll down to the end of the screen and open the advanced mode. There you can add an assembly for deployment. Just simply use the "Add Assembly -> Add Assembly from Project Output" Action and select Ninject.dll.
When packaging the next time your custom assembly will be included in your WSP.
Cheers
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