I'm looking for a mail transfer agent that is free, preferably open source that can run on Windows natively. I've used Postfix before, but Postfix doesn't really run on non-Unix machine.
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I am using hMail server, which works like a charm and is free / oepn source
If you're looking to run a mail server on a dedicated box with open source tools, then for reliability and generally thorough testing of the code you would want to dedicate a system to the task, and for open source there's no match for running on the "native" platform of Linux or FreeBSD.
You don't mention why you have to do it on a Windows box, but the last time I was asked this type of question it was because someone wanted to stick a mail server program on their workstation. This causes issues with reliability, but also can cause issues with being blacklisted. Plus updates and installing/uninstalling software that people use on desktops was always a crapshoot as to whether it would screw up the mail.
If you are doing this on a Windows box because it's what you have available, you could always try running something like VMWare and create a VM to run the program in question. That way you get open source servers running on their native platform, as well as an easy way to back up the state of the machine should you need to restore to another system. More resource hungry but it may save you some headaches.
There aren't a lot of open-source mail servers for Windows; most open source projects on it are ports, often using CygWin to run them, and tend to be slower and non-optimized (and less well tested) and you generally won't get as much of an audience from which to ask for help when using open source on the Windows platform. There are some free programs for Windows but they also tend to have a far smaller userbase.
My advice would be to consider using a Linux box dedicated specifically to acting as a mail gateway or look at using a virtual machine solution on Windows if you must use a Windows box.
an alternative way of looking at the problem:
why not run postfix on a linux box, and have it relay mail to/from the windows machine?
the windows box can then be hidden behind a firewall. or the linux box can even BE the firewall for the rest of the network.