I am not a tomboy, or a girl (the last time I looked) but I can say that being called anything at all has the power to affect you. Tomboys are a good example of how society can try and pigeon-hole people for behaviour that fits into categories and hence make people, (girls in this case) either feel bad about being 'different' or feel they should change themselves, for being different, and thereby loose the stigma of the 'label'.
The ultimate cure is not to be hurt or in any way affected by words, because that will make you stronger within, and the more you question 'labels' the better you will be to think independently of societal slanders, such as the tomboy one. There is of course nothing wrong with a girl who likes to climb trees and play baseball with 'the guys'...in fact there is something 'right' about her...namely she is physically active, and likes to challenge herself.
Now can you think of a better compliment ?