Scenario: Emails forwarded from Exchange server to Pop3 mailboxes. iPhone collects email from the pop3 mailbox. Requirement to delete mail from Pop3 server to prevent the mailbox from becoming full.

These settings on the iPhone will delete the email from the pop3 mailbox when it's been removed from the iPhone:

Settings-->Mail, Contacts, Calendars-->[email account name]-->Advanced-->Remove = "After One Day"

and

Settings-->Mail, Contacts, Calendars-->[email account name]-->Advanced-->Delete from server = "When removed from Inbox"