I am looking for software that can collect emails from many (hundreds, thousands) mailboxes and store it in a local pop3 server. So that I can download all of them from the local pop3 using outlook express.
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Could try using http://pyropus.ca/software/getmail/
I personally use fdm, simple to configure, quick and yet highly configurable
Fetchmail has been a defacto go-to program for this task for a long time. I've used it in many configurations and been pleased, esp to look back and see it still doing it still just doing it's job.
However something tells me that if you're logging into that many POP boxes and trying to funnel them all into outlook, You're doing it wrong.
What is your use case? Maybe the community can suggest a better architecture from the ground up.