I am doing alot of dev on two different boards at the same time quite often (I am writing a sketch for adafruit Huzzah to make it a WiFi<->Serial bridge): a Huzzah and a Leonardo for example, on two different ports.
So I often need to program one after the other and, obviously, I always forget to change port/board settings.
Would it be possible to make them per-window?
If you open the Arduino IDE windows by directly opening sketches or the Arduino IDE application then you can have different settings in each window. It's only when you open windows via the Arduino IDE(File > Open, File > Examples, File > Sketchbook) that the change in setting affects all other windows.