I have a VS 2005 web site that I publish using \"Publish Web Site\", and I clear all the three checkboxes. I also have a deployment project that picks up the published files
Just as a footnote to all of the above answers that resolved the issue via republishing to replace a missing assembly... While i have solved this issue previously with that same solution, i have just encountered another reason for it's occurrence which may assist others.
The AppPool that my site was running under had it's "Enable 32-bit applications" setting set to false. By changing this to true via the "Advanced Settings" dialog of the app pool i resolved my issue.
Hope that helps some other poor sucker.