It's still not clear whether or not each window / sketch should have its own serial port setting and serial monitor.
i now remember that you mentioned that you're working on it. please excuse my ignorance... concerning the serial port: as for copy and paste the port wouldn't matter, and i was originally assuming that one was working on a single project most of the time.
still, "multi-board projects" could become more popular with people starting to explore SPI, one-wire and stuff.
would it be hard to to save board and port settings in a sketch rather than in the application settings? i'm thinking of something like two pull-down menus at the top of each window.