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Uninstalling a lot of stuff at the same time takes too long. If I just remove the directory, it will probably leave some registry records and what else?

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The registry records are enough. As an extreme example, if a registry record tells the system to load a particular file as part of the boot process, and the file isn't there any more, your computer won't boot. In most cases the issues caused by a damaged installation are more subtle than that, but they can still be severe. Probably the most common issue is problems later on when trying to reinstall the same software or a later version of it. Sometimes unrelated software installs can run into trouble as well. –  Harry Johnston Jun 11 '12 at 21:06
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3 Answers

up vote 8 down vote accepted

Sometimes installers put required files in system directories. Uninstallers has knowledge of where these files are and all registry values to be removed. Unless you are sure you know all the directories where these files are, better leave the uninstallation to the uninstaller.

Removing programs by removing directories will almost always result in "leftover" files. This is bad practice since over time these wasted files will accumulate and occupy disk space. This in time fragments data in your hard disk. Then, the more fragmented your hard disk is, the slower your disk read operations get.

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when you do not use the uninstaller, you [maybe] leaving out all the registry entries, appdata files and many other junk in your system
The program installation consists of:
[always] copy files to program directory
[optional]
register the program with OS
add shortcuts, links etc
register certain files with program via registry or other eg doc with word
add custom program info into registry like serial key, program user info and so on
add one or more files into system directories such as %appdata% on windows that saves program data
add one or more startup entries and service entries that start on events such as boot

an uninstaller is a program that has track records of all the actions the program has done and every file created on installation. its job is to remove this data safely and to completely remove all traces of changes the program made to sytem.
when you do not use the uninstaller, you [maybe] leaving out all the registry entries, appdata files and many other junk in your system which [can] slow down your system or cause some problems.
to avoid all this problems and to have the system in a safe state, an uninstall is done.

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adding to what everyone has said:

Besides leftover files and registry entries, you might be unable to install the program again if you need to..
The installer may simply show you that the program is already installed when if fact you don't have the program files...

I remember this happening to me with spiderman game, a few year back.

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