How to remove removed apps OS X URL schemes from system?
How long did you wait until checking the URL list?  Did you reboot?

After you reset the Launch Services database with that command, it will take a few minutes to rescan your system and rebuild the database.  During that time, the existing database will still be used.

I wrote a blog post about using this command to clean up the Open With contextual menu as it would often become corrupted and list applications multiple times.  When I would reset the database, I've seen it take over 30 minutes until the menu is correct again.

If you still have the app installed, or you can reinstall it, you can use the lsregister -u PATH command to unregister an application, which removes the associated URL Schemes.  For example, I still have TurboTax from 2011 installed and in the URL Schemes list, it had a com.intuit.turbotax.2011 scheme listed.  Using the /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -u /Applications/TurboTax\ Deluxe\ 2011.app command, it removed ONLY that registered application from the Launch Services database so it didn't need to rebuild the entire database.  Upon launching the Defaults Apps preference pane, I don't see the com.intuit.turbotax.2011 scheme listed anymore