I have an account on StackOverflow, ServerFault, and SuperUser all linked to the same OpenID. I originally did not think much of it until I noticed I started gaining reputation/badges individually on each site. Are you supposed to gain reputation per each site, or if the accounts are linked is it supposed to be summed across all of StackExchange? I can see all of my accounts in the 'Accounts' tab of my profile, so I am guessing they are linked together (but not merged? if that means anything).
Are you supposed to gain reputation per each site
The only area I know of where your aggregate reputation has meaning is in Area51 when it comes time to commit to new proposals. The more rep you have across the entire StackExchange, the more weight your committment has to that proposal.