The basic reasons for quarantine are:

1. You can review what "infections" you have had, and determine the implications. For example, if I discover I have been infected by a worm that drops a backdoor, then I must decide whether my computer has been "owned". If it has, then there could be anything on it, and the only truly safe course of action is to reformat and reinstall. I might also want to change passwords, bank and credit details and so on.

2. If you have a number of infected files that cannot be cleaned, a list of which files you need to replace is useful.

3. Some malware may contain evidence that could be used in my defence or in the prosecution of criminals. You don't want to leave it active but you don't want to destroy it immediately.

4. By examining the infection you might be able to determine its source and thereby take precautions to prevent it happening again.