I just got back from a week long trip to Kona Hawaii, doing fish distribution/abundance surveys with these folks:
http://www.reef.org/fieldsurv/index.htm
It was a really intense experience. Days were loaded with diving, fish ID seminars and loads of paperwork. (Gotta get all that data into the database SOMEHOW.) It was a great experience and I can't recommend it highly enough. I can't wait for my next trip with them.
In addition to survey trips like the one I was on, they usually do one "discovery tour" each year - a trip led by Paul Human or Ned DeLoach focusing on learning about reef ecology. A ll of the remaining trips for 2003 are full, except for a trip to the channel islands in September. The schedule for next year will be posted soon.
My room mate on the REEF trip collected coral samples for research on an Earthwatch trip to Australia. A list of Earthwatch scuba expeditions can be found here:
http://www.earthwatch.org/subject/scuba.html
You can also check with the Coral Reef Alliance for volunteer opportunities.
http://www.coralreefalliance.org/volunteernetwork/
Or try the Shark Research Institute:
http://www.sharks.org/expeditions/index.htm
Don't expect to get paid for your efforts, but depending on your situation, your costs might be tax deductible. I would be doing this stuff even if I couldn't deduct the costs because the work is important. But If I can get a tax break, I can participate in even more expeditions.
And, oh yeah, I forgot to mention.....take me with you? PLEASE?!?!