We upgraded a solution that uses Crystal Reports from .NET 1.1, to 2.0 and then 3.5 a little while ago and it has been undergoing a full test of all of the functionality. We found that the reports would not load with the following error...
CrystalDecisions.CrystalReports.Engine.LoadSaveReportException: Unable to find the report in the manifest resources. Please build the project, and try again.
There are some other possible solutions/workarounds that I found for this, but in our case it seemed to actually be the namespace of the report files that VS2008/.NET 3.5 did not like. The directory and last part of the namespace involved was "Report Files", i.e. with a space. Changing this to "ReportFiles" has seemingly fixed everything.