Well, I bumped into an interesting build error this afternoon, one I hadn't seen before:

Could not find file 'Microsoft.Windows.CommonLanguageRuntime version=2.0.50727.0'

For reasons I shan't go into here I write production code in VB .NET, however for unit tests I write in C#. This obviously results in mixed language solutions. The error occurs when I reference a VB windows app project in my C# test project using a project reference. This windows project is also published via ClickOnce. According to this knowledge base article the solution is quite simple: use a file reference. Obviously, as I found out, this issue is not restricted to VB projects referencing VB projects; C# projects that reference VB projects are at risk too.

The word out on the street is that you can also work around this by turning off ClickOnce security settings on the project being referenced, which wasn't an option for me. It's important to note that this issue is not intended behaviour, and we can expect a fix in the next version of Visual Studio, codename Orcas.

I'll admit that project references can be problematic, although for the most part they work well at my workplace, but be wary if you are project referencing ClickOnce apps, and don't think you are completely immune if you use C# either.