A while ago I posted about how to make add references of non SQL Server Projects dll's in a SQL Server Project. Well, it turned out that I was not completely correct.
Yes, you can add a reference the way I outlined, but that dll will not be auto deployed when you deploy your SQL Server Project dll.
So in essence if you want to have a reference to a non SQL Server Project dll in your project you need to deploy that dll to SQL Server manually. When you've done that - it will automatically appear in the references dialog in your SQL Server Project.