Any PADI member in this country (don't know about others) is required to fill out an incident report anytime there is injury, illness or whatever that interupts dive activities. The purpose is to document an good as possible what happened and who saw it incase something comes of it down the road. To pit this into perspective, if a diver drops a weight on their own toe and changes diving plans because of it I file an incident report with both the agency and the insurance company. These report are not available to the bublic and the number of reports doesn't mean anything without being able to read the entire thing anyway. Aside from this there isn't anyone documenting this stuff that I know of.
What kinds of things can a dive boat do to get you into trouble?
They can leave without you. Make sure whoever you go out with has a diver accounting system and uses it.
They can take you to sites that are beyond your abilities. Make sure you get a good (include the info you need to make a go/nogo decission) briefing and make good decissions for yourself.
They could give you bad air (I guess) Ask to see their air test data and look at the compressor. Make sure there are filters.
Ask about the crews qualifications. In this country a captain has to be a captain. Elsewhere? Find out if the DM is a DM or if he is just the Captains brother inlaw.
Make sure they have the right emergency equipment O2, radio, first aid supplies ect. Make sure the crew is trained in it's use.
Any other ideas?