jpcummins,
1) The Common Files folders are mainly for components, like Adobe for example, that are shared across software programs.
2) Instead of removing the program folders that you no longer have, I would transfer them to another location, creating a new folder: ie. My Documents\Old Common Files, to see if you have any problems when using other applications. If you do, is easy to transfer them back should you keep them around. After a period, determined by you, without any issues, then you could delete them.
3) Using a program's own uninstaller, usually leaves junk behind. MS' Add or Remove Program utility does a better job, but remnants still remain. I use
Revo Uninstaller, in Advanced mode, to get rid of 98% of a program. There are Legacy Registry keys that Revo does not touch, but for the most part, files, folders and most Registry keys are gone with Revo.
CAUTION: You must know what you are doing when deleting Registry keys found by Revo. If you are not sure or apprehensive about working with the Registry, Add or Remove Program is still your safest bet.