Listed as they come up in my mind, no ranking possible:
1. Where I got my first baitball with sharks ONLY in 20m viz and bumped silly about 20 times...somewhere along off Poenskop, South Africa. Well it's not really a site so I guess I'll have go with...
2. Secret Bay/Bull Point/XXX, Anilao, PI... mating wunderpus, mimic, mototi, bluering and even a flamboyant cuttlefish all in one spot, a cephalopod lover's dream dive. Very accessible dive from shore place.
3. Little Komodo, FakFak, Indonesia. Schooling 'cudas, GT baitballs, jacks, muck, awesome fry action and just loads of life...all in one spot ... for reef life 50% as it should be in the pre-sharkfin world ... unless you go to....
4. Fiabacet, R4, Papua Barat... super fry density with predators everywhere from GTs to mobula rays to tuna, healthy coral growth and even a few sharks deep down... the marine biodiversity capital's offering of what 60% of what reef life should be ... and then you find ...
5. SUPERSECRET SPOT, Pacific Ocean near Indonesia: a real school of hammers and other reef sharks, dugongs, mantas, mobulas, tuna in super fry school action and healthy corals with cleaning stations and usually even great viz. 70% of what life should be and it's still recovering. Ranks lower because of inaccessibility and fishermen also google.
6. The Yongala, rich with life, rays, nappie wrasse, the occasional big shark like tigers, olive snakes thicker than my ankles, all sorts of schooling reef life in a balanced biosphere that has been left untouched. Not very biodiverse but what all reefs should be like in terms of health if there was a perfect world.
7. Tulamben with the Liberty: Wreck with great life including resident trevally school, awesome cleaning stations, muck with the oddest critters on the side and the occasional pelagic visitor like a mola mola, all just 50m from the beach with the main road another 50m back.. Nothing more to ask for in a dive site!
8. Any site in Lembeh when it's hot and no other divers are around! 
9. Bajo Alcyone, Isla de Cocos or the Fridge, Isla de Malpelo, 'nuff said!
10. E6, Koro, Fiji. The colors of the soft corals in 30m viz is just beautiful and then you get the pelagic sharks and the swim through to the Cathedral etc.
11. Tatawa Kechil or BatuBolong, Komodo, Indonesia. Soft corals, reef fish, pelagics big and small
12. Pantar Island, Alor, Indonesia. Huge queensland groupers with great coral growth and fish life... and lots of current. Then you end off with a pier where a bunch of kids are always playing in the water.
13-100 Plenty of sites that deserve mention but you limited it to 11. 