For "Windows compliant programs" a record is generated that lists every change made during installation, including changes to the Registry.

In theory when Control Panel Add/Remove Programs removes a program, it works its way backward through the list to "undo" everything that was done.

In theory an uninstall should remove anything added to the Registry when the program was installed.

One clinker in the theory is that sometimes the record made during installation may "disappear." A few "overzealous" applications in things like Disk Cleanup can cause deletion. "Setup Log Files" is one selection you can click/check to be removed in Vista. These are/include the files needed by uninstall to do a clean removal. The choice is not quite as transparent in WinXP and earlier versions (as I recall), but it is there.

There also are many "third party" letusfixyouup programs that remove great masses of "unused junk" - some of which may be unused at the moment but which might be useful at another time.

A second problem with a simple "back-it-all-out" of all the changes made during installation is that many files are shared between programs. A file added during one program installation may be needed by another one installed later. If the file is already there, in a usable form, the second program will use the one that's there, and will NOT RECORD the addition of that program. If the file is there, but the second program has a "newer version" it normally will be added, and will then be in both lists, but with the wrong version in the first list. (Or with the result that the file added by the first program is no longer there to be removed.)

If the second program is uninstalled first, it should leave the "newer version" of a file that replaced another, on the assumption that something else also uses the file.

If the first program is uninstalled first, it should leave the "newer version" of a file, added after the first program was installed, on the assumption that something else updated - and uses - the file.

Thus neither program may automatically remove a file that was once or ever "shared" by the two programs. This could lead to some "clutter." The Control Panel uninstall appears to make some additional checks to resolve whether or not a file is still in use and this is sometimes successful. If Windows can confirm that the file is not in use, it gets removed; and if it is still needed, it gets left. When Windows can't make a decision, you sometimes will see a "This file may be used by another program. Are you sure you want to delete it?"

In the ambiguous case, I usually assume that if Windows can't be sure it's needed it probably isn't; and as yet I have not had a "file not found" error from doing so. (Note that I don't do a lot of changes, so I don't have a large statistical sample on which to base an argument that it's always best to delete.)

Since all the files truly necessary for Windows are on the disk before any programs are installed there is no reason for any program to be adding a "Windows critical" file, so a program uninstall should never remove one. The worst case is that a single "add-on" program (or program suite) may burp and belch a bit if you delete one that the program needs, in which case you just put the file back (i.e. usually - reinstall the "other program" that needs it).

To answer Joe O -

The official advice from Microsoft, and from most of the "establishment advisors," is that "registry cleaners" are of little use. Controlled testing has failed to show any significant actual improvement in performance after using the popular ones on machines deliberately "trashed up" before running the cleaner. Although the machines tested were pretty messed up, they may not have been quite as thoroughly mangled as someting "Joe the @#!%" might be running. None of the "cleaners" I've looked at (fairly casually) tell you much about what they actually do, so general statements about whether they do a specific kind of "removal" are speculative, at best.

Most of the authoritative advisors say they're unlikely to hurt anything, so "do it if it feels good." (Almost always good advice.)

As noted, some "system cleaners" may remove seldom-used-but-sometimes-useful things like installation logs, error logs, and .cab folders, which can impede subsequent maintenance of the computer; but this isn't likely to be too serious as long as you (like everyone always does, of course) keep your original installation disks handy.

John