Some such apps have been delivered in malware-like methods (as part of bogus Flash Player updates, for example), which immediately makes any other claim they make suspicious. Countless "buy me and clean your Mac" popups until users manage to banish them from their systems.
Other apps have been accused of being overly-aggressive - in order to deliver promised results, they must find something to be deleted.
I have used photo duplicate-finding apps from time to time, but the work that goes into deciding whether the app has truly found duplicates, and which of those duplicates to delete can be daunting when you have as many photos as I have.
For the most part, the "cruft" some people obsessively chase it totally harmless - a few KBs of configuration data left behind after an app has been deleted. If there's no app to call that particular file, then the only harm done is the space being occupied. There have to be a whole lot of orphaned files of that size and sort to add up to anything that will make a dent in the typical HD.
From my perspective, the only point to running some of these apps is to feel like your Mac is "sparkling clean." To some degree, that's like feeling your kitchen countertop is "sparkling clean" - a closer examination may show that "clean" is more of a feeling than a reality.
