how do I delete an Eclipse project when I've already deleted the folder and contents?

Try removing directly the project within your workspace, within:

<workspace>\.metadata\.plugins\org.eclipse.core.resources\.projects\

as mentioned in "Where in an Eclipse workspace is the list of projects stored?"

In my case the project was completely removed yet still referenced in Eclipse. Thing is, the file holding the Working Sets configuration was the culprit. What I did was:

1. Shut down Eclipse
2. Open .metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml
3. Find the faulty <item> tag and remove it
4. Start Eclipse

Don't have rep to comment directly on @VonC's answer yet. But here is how it worked for me.

1. removed the projects from <workspace>\.metadata\.plugins\org.eclipse.core.resources\projects\ As suggested above

2. Try to open each project, clicking "ok" to all th errors Now it seams it is gone, but if I try to import a new project with same name Eclipse claims they are still there.

3. in the project explorer press 'F5' to refresh. N ow eclipse realises the project is gone, and asks if it should remove the project from workspace, after accepting the project is now gone.

Maybe step 2 can be skipped, I have not tried.

My eclipse: Luna Release (4.4.0)