The main reason why those tools exist is for paranoid people. Leaving those preference and plist files there will not "rot" your system which is what the person I replied to was talking about. If cleaning OSX was so mandatory like removing these plist files then Apple would have included a tool that would do so. They might take up a decent amount of space which could lead to low space on the HDD, but other than that they have no harm on the operating system performance. The only way they could lead to some sort of negative OS performance is if they are always running, and even then you can easily check what is and isn't running.
What part about the daily, weekly and monthly maintenance script did you not understand? Those are OS X's own scripts that run to do some system maintenance. You need to have to run those because one of the things it does is rotate the logfiles. If you don't do this you'll end up with huge logfiles that hog down the system.
Leftover plists can cause other problems when you reinstall the software. The reason they're not removed in the first place is because of this, you can install the software again without losing your settings. Due to differences between versions this can cause strange problems. In the ssd age you want to have a clean as possible drive because of the performance degradation that sets in when the drive fills up.
Again, plist files are just one of the examples given, there are quite a lot of other things in OS X that can cause problems when not taken care of (like logfiles).
Is AppCleaner an automated program? I have about 50GB free on the factory 120GB hd.
It has a monitoring process running in the back that monitors the system for deletion of apps. Whenever you delete an app it will locate corresponding files and prompt a dialog where you can deselect everything you do not want to remove (so if you want to leave the plist files simply deselect them). When you confirm the selection it will put everything that was selected in the trash. The automation is the monitoring process running in the background.
I just cloned the drive to a 7200RPM 250GB drive, but if it's all bogged down with crap, I may want to do a fresh install.
Cloning installations and putting them on new hardware is quite known for things like that, especially when you've cloned the installation a couple of times. You might call that OS rot too. A fresh install might do wonders in this case. Whenever I get a new machine I see this as a great opportunity to check my current installation and do a bit of a cleanup. Mostly I'll partially restore the system (applications and settings, sometimes just applications) and go from there.
AppCleaner is garbage and leaves files behind. If you want a good uninstaller application then get AppDelete.
AppDelete is as much garbage as AppCleaner because all of these apps leave things behind. That's why the corresponding developers put a warning about this in their disclaimers. However, AppCleaner is freeware, AppDelete isn't. Since these applications never cleanup everything there is, it's a bit of a waste to pay for it. The reason why they leave files on the system has to do with things like filenames, the information they have about what files went where and user rights. Those apps are not foolproof.