Gallery KK, the Gallery the M9 came with it terrible.
VLC Media Player, like the desktop one you can change languages, subtitles and video streams on the fly.
FireFox, if you use it on the PC, you can since your bookmarks from the PC to the phone.
BBM, we all know what that does.
Office Lens: Takes pictures of an area and adjusts them into nice little documents.
TaskManager, a very nice looking device manager that lets you close all apps and clear ram with one click.
IR Remote, lets you control your TV with the phone.
CCleaner, program that like the PC one, cleans out all the junk from the phone.
SoftKeyZ, lets you customize the 3 Navigation Buttons at the bottom.
Google Now Launcher, I prefer this to Sense as this is very clean once you turn off the Google Now Feed to the left.
TuneIn Radio, lets you listen to radio from anywhere on Earth.