You will have to start regedit.exe and go to the following section:
HKEY_CURRENT_USER\Software\Allround Automations\PL/SQL Developer\PlugIns\VCS\ProjectHistory
Here you can delete the items you no longer need. Note that they are numbered, so if you have 5 projects and want to delete number 3, you will need to rename 4 to 3 and 5 to 4.