How does one know that the cleaner is not part of the problem?
If the cleaner makes a mistake it IS part of the problem and can't be relied upon to function properly. Tools that don't work aren't tools at all.
Or does the registry just get dirty with use, kind of like motor oil?
You could view it that way. Each time you dbl-click a program icon, an MP3, a document, a video, whatever... an entry is added to the Regy. Bloat. A little ridiculous but it is what it is. CC attempts to remove much of that bloat if it knows where to look.
a single program could not interpret what a registry value means- for example, if a program stores a filename to create in the registry- a cleaner would come along and delete it, since the file doesn't exist. So next time the program that uses the key starts- who knows what it'll do.
App creators are SUPPOSED to put program value items in the appropriate hive key: "Software/MyCompany/MyApp/SectionName/KeyItem=(value)", similar to the old INI file. They don't always follow that rule. Take the "SharedDLLs" key for instance... it's a dumping ground for all sorts of trash. MS, Lightscribe, Adobe put all kinds of non-DLL files there: TXT, DAT, EXE, BIN, SCR, HTML, CHM, CNV, OLB, AX, TTF... and that's just in the first ten pages (mine has 4500 entries.) A program like CCleaner "verifies" these entries are where they say they are. If they aren't, CC will indict the Regy entry as invalid and recommend entry deletion.
One mistake in 4500 and CC earns the label of "unreliable". I found two errors (two files identified as missing that were exactly where they belonged.) Given that level of quality I wonder if I should turn CC loose on the rest of my Regy... which explains the nature of my "feel good" post.
Matt