Ninite Pro can uninstall applications too. Just use the /uninstall switch.
Here's an example command to remove iTunes from the computer you run it on:
NinitePro.exe /select iTunes /uninstall
The /uninstall switch also works with Ninite Pro's remote mode:
NinitePro.exe /select uTorrent /remote file:machines.txt /silent report.csv /uninstall
This would remove uTorrent from any machines listed in machines.txt and write a CSV report of the operation.