I have an ASP.NET MVC 2 application.
I have created this issue as a bug on Microsoft Connect. If anyone experiencing it could vote it up https://connect.microsoft.com/VisualStudio/feedback/details/637071/publish-web-feature-not-including-all-dlls then hopefully we'll get something done about it.
I have created a new Connect bug here https://connect.microsoft.com/VisualStudio/feedback/details/731303/publish-web-feature-not-including-all-dlls
I've also attached a solution and detailed steps to reproduce this issue. Lets hope this time they won't close it as Can't Reproduce.
Vote for this connect issue if you experience the missing dll problem.
My tests show that the external assemblies get published when I have a reference on them in the web project. I do not have to write any dummy code to make it work. This seems acceptable to me.
I agree with Nicholas that this seems to be a bug in visual studio. At least it escapes me what the reason for the behavior could be.
None of these answers are sufficient in my mind. This does seem to be a genuine bug. I will update this response if I ever find a non-hack solution, or Microsoft fixes the bug.
Update:
Doesn't seem promising. https://connect.microsoft.com/VisualStudio/feedback/details/731303/publish-web-feature-not-including-all-dlls
I had this same problem today. I published my web project and realized that not all of the reference DLL's were there. In particular, the indirect DLL references.
It turns out that the directory in which I was publishing to was out of disk space (network share). I had just enough space to publish all the files except for few indirect reference DLL's. The sad part is that VS08 didn't throw any errors. It just published the files are usual. I cleared out some HDD space and everything worked fine.
I didn't find the HDD space issue until I tried to manually move the DLL's over.
If you go into the ExternalAssembly2 reference property list and change the "Copy Local" to "True" i think that might solve your issue.