The BlackBerry Help Center page on removing your application using the command line says that the command line blackberry-airpackager utility supports an -uninstallApp argument. In the version I downloaded (as part of SDK 0.9.1) this option is actually on the blackberry-deploy utility (presumably having been moved).
Also, the arguments shown are now incorrect. After checking the help output (by running the utility with no options) and experimenting a bit, the following pattern worked:
blackberry-deploy -uninstallApp -device 192.168.40.128 -password XXX -package MyApp.bar
If you don't have your .bar file, you can use the Package-Id instead. If you don't know it, you can discover it using another option:
blackberry-deploy -listInstalledApps -device 192.168.40.128 -password XXX blackberry-deploy -uninstalledApp -device 192.168.40.128 -password XXX -package-id YYYYYYY
There's also another approach which may be much simpler in a given situation. The simulator runs a little web server accessible via http and https. The http one seems useless, but if you go to https://192.168.40.128/appInstaller.html (substituting your sim's IP address) you'll see a few useful things.
Your package's Id is available in numerous places including the console output of the deploy tool, the MANIFEST.MF file inside your .bar file (which is just a .zip file with a different extension), or you can find it by clicking on the List button at the end of the above appInstaller.html page.
Once you know it, enter it into the Package Id field and click Uninstall. [This interface was removed in later versions, so use the command line approach described above. -Ed]