As Tom announced here, he's revamping the reputation system, starting with site activity reputation, which is complete. You can see how your rep is being calculated here:
Check Your Site Activity Rep
So where did all the rest of the rep go? Badge rep has been temporarily taken offline while the badge reputation system is also overhauled, but as Tom mentioned in his post, he expects it to be reactivated next week.
Among other things, this fixes the accidental misattribution of badge rep from a few site glitches a year or so ago, but this almost only seriously effects people who wound up with 187 Devoted Badges or similar mistakes.