Pretty much anywhere in the Indian or tropical Pacific Ocean. The whole countries of Indonesia and Philippines are like one big dive site. Malaysia--on the island of Borneo you have Sipadan which they only give out 120 permits a day; you can see basically every rare tropical creature that you usually only see once a trip on vacation on one dive alone.

Honestly, there is so much out there that hasn't been explored or hasn't made it into a brochure--typically if it's talked about, it's already in danger of being touristed out and it's just a matter of time.

Scuba diving travel guide - Wikitravel