The POP3 protocol tags each message with a unique identifier (given with the UIDL command). Outlook and Outlook Express both seem to ignore these UID's and if a transfer fails part way through will re-download the same message again and again. Users complain to me that my server sent them 300 copies (for example) of the same message, when what really happened was that Outlook downloaded the same message 300 times, each time thinking it was new. Using UIDL would avoid this problem so easily.
My second biggest pain from OE/Outlook is their interpretation of the CRLF/CRLF delimiter between the message header and message body. The STD's say that a CRLF/CRLF pair is the delimiter between the header and body, but they do not mandate that the CRLF/CRLF pair must exist. Both Microsoft MUA's require this double octet pair and will crash if they don't find them. This is the biggest problem which causes the first problem I described. Lotus Domino does not include this delimiter if a user sends a message with a subject but no body. While I think both products are flawed in this regard, I'd like to see both fixed as loose interpretations of the STD's result in better software for all of us. These two bugs are the biggest things I'd like to see improved in both OE and Outlook.
I don't have an MSDN membership, so I can't test to see if you've already corrected these things, but I wanted to bring them up just in case. Thanks very much for taking the time to listen.