For the Great Barrier Reef I used Down Under Dive, they were running a promo for AU$90 that included one intro dive and snorkelling on the reef . Lunch was also thrown in as well as great entertainment by the crew.
You can pay extra to do two dives but we stuck with one dive and then snorkelled for about two hours in total.
For the Whitsundays we used a Maxi yacht called Broomstick. Its a retired racing boat so it only holds about 20 passengers. If you want to just go on the beer there are other boats that take up to 60 people. Very young crowd on these though. We stayed on the boat for two nights and had a great time. You get to know all the passengers and go snorkelling a couple of times. Food is superb, quality and quantity. There are boats that focus on diving as well, more expensive obviously.
If you are travelling on your own OzExperience is handy cos you get to know people. On the downside you can be stuck in a place for a couple of days waiting to get a seat on the bus. Plus they stay in some really bad accomodation in certain towns. We used Premier buses and just rang up the day before we wanted to move on and never had any problems. Plus you then get to choose your own accomodation.
One piece of advice is not to try and see every town on the east coast. Most of them are mirror images of each other: sea, beach, main street. Ones I recommend are Noosa and Port Douglas.
Also recommend going to one of Peter Liks galleries. Even if you aren't into art, his stuff will amaze you. If you want to buy make sure you have loads of room on your credit card!