How after you ask your first question on SF/SU/meta you get a bronze badge on Stackoverflow as well (and vice-versa)? This would bring the sites closer together, encourage people to associate their accounts, and just be plain fun. I agree that reputation should definitely be separate across all site, but a little badges thrown in for fun would be cool.
Something like "Supporter" badge on SO for asking your first question on meta (although that badge name is already taken, so we'll have to think of something else..), or a "all-around-geek" badge for having asked a question on all of the sites? (help me with the badge level and names) :D