When you create an installer project via the VS wizard it will generate all the dependancies it finds in the main project.
It can arrange registering off COM dlls.
You must ensure .NET dlls you added which were additional to standard .NET framework (1.0 or 1.1? I guess they all have same but you could check this) are included in the installation.
Your addition .NET dlls can be copied into the bin of your app so they are local to that app only. IF you need them to be in the GAC then they need to be stong named - but you don't need to put them in there.
IF you know all the dlls needed you can do all this manually simply by copying them to the client machine (obviously COM dlls always need to registered in the trad way).

Sometimes you may have used a component only to remove it but has it been removed from the referenced assemblies?