This might not be easy. I have a similar project planned sometime this year. I also have a Windows based mail server (Imail) and I'm planning to covert to Fedora server running Qmail + Squirrelmail.
I know that Imail and several other Windows based mail servers use a special format to store the mail messages. I don't think there is a good way around that unless you can find a conversion utility that happens to accept your specific mail format and convert it to one of the *nix standards.
The approach I'm going to do is slowly migrate each client, one domain at a time. I will instruct them to download all their mail (I have some clients that have never logged into to their account and thus have gobbs of junk taking up space) via POP3. Once the mail is "clean" from the original server, I'll make the switch to the new server. I'll have the new server start accepting mail so they will have new stuff go to the new location during the migration period. That also gives you the ability to check out settings for each client as the migration processes.
I figure at some point, you'll have to just "dump" some addresses that aren't being used.
If you have thousands of clients -- it might be worth some custom programming to do the conversion for you, and saving you LOTS of time. For smaller numbers of accounts, just migrate over one at a time.