We disable the accounts. Their "descriptions" get updated to indicate the date of the departure, and they get moved in the AD hierarchy to a folder depending on what state of departure they are in (gone+email forwarded somewhere, gone+pre-archive, archived).
We have a large quantity of complex files and folder hierarchies. If you delete the account from Active Directory, and file/folder with explicit per-user ACLs will have that ACL data displayed as a SID. And I have not found any way to figure out from a SID which account it used to be -- because the account has been deleted.
This way when people are looking at ownership/permissions issues which are behaving oddly, we can see (and delete) ownerships and permissions of people who are no longer present.
If you delete a user and later on you discover that he or She have encrypted some files and folders using EFS, you will not be able to decrypt them.
Update, much later: I learned from a colleague who is undergoing an audit from Microsoft that accounts in your AD require a "per-seat" license (if you are swinging that way), whether or not they are a real person and whether or not the person is still present. So there is an argument to be made for deletion!