I think Wild Aid is one of the best conservation organizations as they are attempting to "stop the buying so the killing stops, too," and they do a lot of (great) work in China, ground zero for anti-conservation.
I'm also a fan of Sea Shepherd because sometimes you can't just wait around and hope others stop their killing.
Nature Conservancy and Ocean Conservancy (not related) work world-wide to preserve species and their habitat, while Defenders of Wildlife works primarily in the US and North America.
If you want to stick more to organizations that are more directly connected with diving, then there's Shark Savers.
Of course there are a million more organizations, but these are all large enough to make a difference, while still being well-regarded.