I have one project that seems to be missing the WEB-INF/classes folder, with the generated class files. How can I force this to regenerate?

In Eclipse, make sure you have the Build Automatically option checked in the Project menu. Select the project and select Clean... from the Project menu. Once the project is cleaned, it should automatically do the rebuild. You also need to make sure in the Properties->Java Build Path/Source tab, the Default output folder is indeed pointing to the classes fold you are checking.

Properties->Java Build Path/Source tab, the Default output folder

This was the fix. I was also missing JRE on the build path for some strange reason. Thanks!!