Which one to chose and WHY when done with running anti-spayware or anti-virus programs?

The general rule should always be to select 'quarantine' because it is possible to make mistakes or to remove 'false postive' files (malware flagged where no malware, in fact, exists). You will be glad for the 'quarantine' area in case you need to get something back and accordingly, should allow a suitable time-to-live period for any such deemed malware items.

You will sometimes notice that the recommended action may be to 'delete' when the default action you intend is 'quarantine. This often happens with (tracking) cookies, which will easily reinstate themselves if they are ever truly needed.