Shortly after I started playing online poker in the PartyPoker heydays their site went down when I was the chip leader in a $30+3 tournament with a couple hundred entrants. Back then I considered myself to be lucky to be in the chip lead at any point in the tournament. So I was very uneasy when it went down, especially when I was leading. Everyone said to just be patient, so I waited. Within a day or two I was compensated very nicely!
Most sites if you look under their tournament rules will have information on what happens during a tournament cancellation (if it is a problem with the site/tournament and not just your internet connection). Found the info for Full Tilt here:
Online Poker at Full Tilt Poker - Tournaments: Tournament Rules under point #31.
-Mike