The two areas in which these types of accommodations are most prevalent are French Polynesia (aka Tahiti) and the Maldives. In general, if you want the stereotypical OWB with all the bells and whistles--including crystal clear water and glass floor or coffee table, and more upscale building materials and furnishings--these 2 areas will have the most options.
There are a few exceptions, of course, one of which is a brand new resort in Fiji called LikuLiku (http://www.likulikulagoon.com/)
Another gorgeous place for an OWB is Aitutaki Lagoon Resort, in the Cook Islands http://www.aitutakilagoonresort.com/
In the Phillipines: http://www.elnidoresorts.com/
Other resorts with OWBs do exist throughout the world--just be aware that these may not all be at the same level of luxury or in as tropical of a setting as the OWBs mentioned above. Not to say they would not still be wonderful places to vacation--just perhaps somewhat different from the commonly seen French Polynesian overwater bungalow. Here are a few to consider:
Coral Lodge-- San Blas Islands, Panama http://www.corallodge.com/
Punta Caracol Aqua Lodge-- Bocas del Toro, Panama http://www.puntacaracol.com/
9 Beaches--Bermuda http://www.9beaches.com/
Hotelito Desconocido-- near Puerto Vallarta, Mexico http://www.hotelito.com/
Anthony's Key-- Roatan, Honduras http://www.anthonyskey.com/
Coconuts Beach Club--Samoa http://www.coconutsbeachclub.com/
Glover's Atoll Resort--Belize http://www.glovers.com.bz/
St. George's Caye Lodge--Belize http://www.gooddiving.com/
