Last year, I had planned on flying over the great barrier reef in a small rented plane, but unfortunately, we hit some bad weather as soon as we took off, and had to do an immediate U-Turn and land back at the Cairns airport.
This year, the weather looked quite suspect too, especially with the bad rain the previous day, but we got lucky: there was a ceiling of 1600ft, which was high enough for a flight over the ocean.
I ended up renting a C172S, along with a commercial pilot/CFI to be responsible for air traffic control and radio in general (I'm not licensed to fly an Australian plane), and flew with Jennifer towards Green Island and towards Port Douglas, before heading back to the Cairns airport.
The views of the reef were quite nice, and flying just 100 feet under the clouds in VFR conditions with no traffic separation from other traffic (including IFR) felt quite wrong, but that's apparently the Australian way from what I'm told.

You can look at more pictures of the flight from Cairns over the Great Barrier Reef