In terms of chemical composition I don't think there is a big difference between them. DOT4 just has a higher boiling point than DOT3. As far as I know you're safe to use DOT3, 4 and 5.1 in your brake system without any problems. If you want to go to DOT5 though (which is silicone based) I think you've got to replace some of the seals as well as flush the whole system.
Cheers,
Phil
Cheers,
Phil