My favorites are:
-BBC The Great Barrier Reef (you can watch two of the three episodes for free on youtube
http://www.youtube.com/watch?v=b_d3LFvc8HQ
http://www.youtube.com/watch?v=SA5qhC_Y1sw
-bbc south pacific
-coral reef adventure (IMAX movie)
-bbc blue planet
-the living sea
-bbc wild indonesia
-bbc wild caribbeans