Indirectly coming from the From Squid A Day blog, is io9's summary of monitored noises of the deep Pacific:
Of course, I'd be remiss if I didn't mention the preferred fanciful explanation for the Bloop. It just so happens that the origin of the Bloop noise is located in the same general part of the southern Pacific Ocean as the location H.P. Lovecraft gave in his 1928 short story The Call of Cthulhu for the underwater, extra-dimensional city of R'lyeh. The coincidence isn't that spooky - the two locations are about a thousand miles apart - but the two are close enough together that Lovecraft fans have suggested the Bloop might well be the sound of a snoozing Cthulhu.
Honestly, at this point, it seems roughly as believable as any other explanation. It's really just nice to know the oceans are still keeping at least a few seriously hardcore mysteries.