win.ini is another file used by 16-bit applications (aside from system.ini). I found this file on both XP and Server 2003 when looking at the msconfig.exe.
On a side note, I noticed that the calculator program stores program settings on the file, win.ini via the function, WriteProfileString(), and reads it using GetProfileString(). On the MSDN page for WriteProfileString() ( http://msdn.microsoft.com/en-us/library/windows/desktop/ms725504%28v=vs.85%29.aspx ), it specifically states that this function is for 16-bit Windows compatibility, and that it suggests to instead store the values onto the registry. Unfortunately, I don't know where on the registry I would store it instead.