I have created a plugin and used a reference to another project (DLL) I have created. The problem is when I try to run the plugin, I get a CRM error saying:
I have a blog post here on how you can put it all in 1 DLL without ILMerge: All References within CRM2011 plugin. We've yet to have a dll issue since we started doing this.
NB this approach rules out the use of Sandboxed mode (i.e., you will not be able to use this approach should you require your plugin to work in Dynamics CRM Online).