You would have to delete their subfolder in the Program Files folder. They will not show up in add/remove programs unless the image is made after the program is installed (and they have their registry entries in the OS Boot Drive).
Anyway you can use the likes of Macurium Reflect every month or so to make a new image of the OS Boot Drive so you always have a new image to back up from.
There are a few exceptions where the files in the Program Files and Program Files (x86) folder can be used such as Steam and EA Origin which can have ~100's of GBs worth of game installation files. I document Steam here (I've still to write the EA Origin guide but have the screenshots):