I first installed Eclipse and the JDE along with the simulator for the Tour on VZW last September. I haven't touched it since December (I had some big issues come up that I had to deal with).
Anyway, I had some MAJOR trouble getting my head wrapped around the BB development APIs. That resulted in my restarting several times. Each time resulted in a NEW app appearing in the simulator.
EVERY attempt I've made to remove these apps has failed miserably. I even tried using Blackberry>Erase Simulator File>Erase All. The next time I ran it, the apps were still there.
Find the simulator folder, browse it and you will see the files for the apps (cod, rapc, etc. - for example HelloWorld.cod, HelloWorld.jar). Delete those file, use Erase All option and it should be fine.