I have been using incoming mail settings on a number of sites within a site collection for the better part of a year, however it broke on Monday and I have not been able to find out why. It is broken on many lists scattered accross all of the sites in my site collection (they are all broken). I have doublechecked everything and I can see the emails get dropped in to the mail dump directory (on the sharepoint server) that I specified in the Central Administration Console. Once the email is dropped in the folder, the timer service comes and picks up the email. After that, the email disappears and never shows up in the list where it is defined. I have checked the email settings in my lists and they have not changed and are still correct.
Are you getting any errors in your event logs or sharepoint logs? Once common cause for this is the "Unknown Alias" error. See documentation and fix here: