For the most part, I haven't had too many problems with the stock Email app on my Moto Droid. I have both ActiveSync (Exchange) and POP3 accounts set up and never have trouble with ActiveSync. But for some reason, with the POP3 account, sometimes the app gets into this endless loop and won't stop downloading the exact same message and showing it as unread.
I'll open the message, delete it, and then next time the app checks for new e-mail, the message is back again as if I'd never opened it in the first place.
Usually the problem seems to go away if I either (a) delete the message from the message list without opening it, or (b) delete it from within the message and then immediately hit "Load more messages". But neither of these methods work all the time; sometimes the message still comes back!
I'm wondering if anyone else has experienced this and knows why it happens (I assume it's got to be some connectivity issue - I do know that the Email app flakes out a lot due to 3G/WiFi switching, but that's hardly a complete explanation), and if there's any foolproof way to either ensure the message is deleted "for good" or to prevent the problem from ever happening in the first place.
Unfortunately I've never been able to reliably reproduce the issue - it seems to be random or at least intermittent.