YPOP is excellent so far. Just few pointers about possible improvements. Here I am adding them without categorizing them on priority like "high", "low" etc. Few of them will really not be so essential unless we are sitting idle and we don't have to do anything.
1. Selected message re-retriving (in case if something is not successful, for eg. text displayed as raw html)
2. A prompt for power users, which will let the users get information about the mails just like SQL prompt. For eg. "all mails on so and so date", "number of mails in this week"
3. I haven't looked into the code but I feel that performance can be further optimized.
3.1 Selected "on the fly" download. For eg if the mail contains a few MB attachment (which should be configurable), then the attachment can be downloaded on request by the user or when things are idle.
3.2 Priority based downloading. First header, then contents, then attachments etc. If everything can be in multi-threaded mode, it would add lots of sence.
4. Security enhancements for locking the configuration. (can introduce a password for changing the setttings)
5. Statistic summary about use of the Ypop. Numbers of message downloaded, sent etc.
6. Spam control at conversion level ( Seems naughty idea, isn't it?