i can notice a severe performance drop when playing war commander (a basic flash facebook game) in normal window inside the browser, however, if i put the game in fullscreen, it works perfectly.
i use firefox and have a gtx260.
Remember when the game is full screen, your GFX card is only processing the game, but when you are in window mode it has to process the game and the desktop. At least that is how I understand it. I could be wrong...