OnyX and TinkerTool are both simply a GUI front end to what you can do in Terminal. And the tasks are actually the same things that now happen automatically since 10.4.4 ( run the periodic Unix tasks/jobs ). Or they do the same thing as Disk Utility ( repair Permissions ). Some access settings that Apple chose to hide from us for whatever reason. I use both in their Tiger iterations.
Preferential Treatment doesn't actually do anything to your prefs/plist files except read them. It checks that they are valid XML documents. Period. Even if it finds an invalid file, it will not offer any way to edit/change it. And it doesn't know what the values in the file should be so don't expect it to tell you that a program is crashing because one of its prefs has a value of 1,000 instead of 1. It's mainly for discovering that there is a corrupt pref file somewhere. I use it about once a month.
I think MacJanitor is mainly for finding/deleting duplicate files. Trouble is, there may be a reason for there being a duplicate or you may mis-read which one is not needed. I am very skeptical about these kinds of "cleaning" utilities. OTOH, I am going to need one soon to verify that one drive has all the files found on several partions so I can erase/re-use that space. I have never used it.
I have no experience with Main Menu but I use another "menu" app that allows me to have anything/everything I want in "regular", hierarchical, text ( with icons ) menus. Most of these apps don't change anything in your System, they just use and display it in different ways. They are no more dangerous than any other app.
Disk Warrior is a totally different animal. It should never destroy anything. But it does repair your main System directories and move files around to clean up wasted space. These two tasks can destroy your disk info if done incorrectly. But one of the reasons you will pay a significant price for DW is to support the developers in their quest to make sure what it does is as safe as humanly possible. Many people swear by DW. I have, so far, not had a need to buy/use it. But I do have/use other commercial utilities.