Hi blake05,
Actually, I am using ILMerge, but it only merges and does not obfuscate. In fact, I have to use both, because the Community Edition of Dotfuscator does not support merging.
Anyway, when I use ILMerge, on all the DLLs in the bin\debug folder, or even just on all the Microsoft.*.dll files, it fails because it's missing the Unity assembly.
Now that I know where the Unity assembly is, I can try again. Just haven't gotten around to it yet.
I am curious if other obfuscation tools (open-source or otherwise available for free) are easier to use than Dotfuscator and can be integrated in a build process, but I guess that's a subject for a different thread.