Booth get's upset when anyone calls him by his first name. Remember he got upset at Cam a few times because she called him by his first name. But i just rewatched my season 4 dvd and in the season premiere Yanks in the U.K part 1 and 2 and at the end of part 2 brennan did call Booth Sir Seeley so if you count that then yes brennan did call booth by his first name but only that one time.=-)
Yeah, I don't think so. It'd sound SO weird. Booth is BOOTH. He's only called her Temperance a few times. To Booth, Brennan is either Brennan or of course (most commonly), BONES. :) That's the way it should stay.