The "helper" apps do in fact provide functionaity that Apple does not. Yes, they can cause problems in an upgrade. But -
ASM restores the nifty way one can quickly change applications, harking back to OS 9 - so you don't have to scroll through the dock. I have a large monitor; ASM makes it much easier than covering a lot of screen real estate.
Tech Tracker keeps my applications up to date, and deals with non-Apple apps as well.
TinkerTool provides easy access to the interface without having to make changes in the Terminal.
Flip4Mac of course lets me view WMV files, which some news sites insist on using for their videos.
And Sophos has done a better job of catching viruses in email attachments than anything else Apple has provided. My friends who operate Windows machines particularly appreciate it.
Menu Meters lets me know my processor usage and available memory - while I have 6GB of RAM, still, I can run short when working in Photoshop. It tells me immediately if there are incoming or outgoing transmissions - helpful if I wan't making them - especially if my drives are reading or writing as they happen. And they help me see the speed of my uploads and downloads - perhaps not vitally necessary, but I like them.
Microsoft Mouse lets me use a trackball that is far more useful and far superior to any of Apple's "mice" or its trackpad. I have 2 more in storage if this one ever wears out.
I am not surprised that some applications no longer work with the upgrade to Mountain Lion, despite the fact they all worked with Lion. They caused no conflicy problems in Mountain Lion v. 10.8.0 and 8.1 (though Onyx and Cocktail don't work with Mountain Lion and are both gone now) - and began showing problems only with10.8.2.
And yes, I use software to get rid of all the components of an app that I discard, so it wasn't "leftover" components causing the conflict.
In fact, I find myself wishing I had stayed with Lion. Mountain Lion's Notification Center is OK but not necessary. I hate the new email headers, and the unified search/URL bar in Safari is crap. I miss the scroll arrows and the ability (via "helper apps" like Cocktail that worked with Lion but are no longer compatible) to place them together at the top & bottom of a window. For all the touted "improvements" in Mountain Lion, it has not been worth either the money or the headaches.
So what I have "learned" is perhaps Apple's direction in its OS is not serving my needs, and I should just stay where I am. And I speak as someone who started with Apple back with System 5.
OS 10 offers significant technical advances over OS 9, it is very true - I am well aware of them. But Apple's failure to recognize some of the best user interface features when it jettisoned OS 9 was bad. The "tinker" apps go a long way toward making up for that. I'll keep them, thanks.
And as far as I know, it was still the reinstalling of the OS10.8.2 combo updater downloaded from the Apple site (not the App store), and running permissions repair after, that fixed the problem. The other steps did not, so I do not believe they were the cause of the conflict.