If I have multiple savings accounts, do each account get the 6 transaction limit imposed by Regulation D, or am I limited to 6 transactions for all accounts combined?
The restriction is per account, not per person. For example, if two people co-own an account, they still get only 6 transactions per month, not 12. Likewise, if you own two accounts, each one still gets 6 transactions.
In any case, you should read the terms of each of your accounts to see whether your institution even cares (i.e. imposes some sort of penalty) when you exceed these limits.