What can I say - I just ended up missing it while it wasn't there. Anyhoo, it's back now and everybody will carry straight on from where they left off; if you had 1337 reputation points before the system was disabled, you'll notice that you still have that amount now that it has been re-enabled again.
For those of you whom have registered since the reputation system was disabled, you can hand out "rep" points to posts that you find funny, witty or helpful by clicking on the little
icon below every user's avatar, post count and join date information.
Cheers!