There are a ton of things you want to check. First, go to NADA and enter all the options. A lot of boat owners are underneath their loans and are selling the boat on consignment because they need to sell it for the amount owed on the loan, not the actual value. There are some great deals out there, but buyer beware.
Open the motor cover. Does it glide back into place easily? That will tell you how many times someone has opened the motor cover (if has wear and tear...beware).
Look at the motor mounts. Do they line up with stains or has it been moved or is not straight (this will tell you if there has been major engine trouble and if the motor has been pulled)
Look at the condition of the bilge. If it is super dirty or worn: it is a bad sign that the owners did not take care of the boat. The bilge is key in determining what has happened to the boat. Most mechanics will leave things behind if its a major job. Look for any sign of debre.
Take a look at all the comparments and storage in the same manner. Look for signs of stupidity. You will find them on any boat.
Take a good look at the entire hull. Look at the trailer boat guides and the hull to see how the owner did on trailering it. There will be signs of wear to the hull if the owner didn't learn how to trailer the boat efficiently. Look really closely at the hull. Just forward of the supports on the trailer you will find gouges in the hull if the owner did not take care while trailering it. Bad sign.
Look into the exhaust fittings on the back of the boat (both of them). If you see debre, black powder, or even rust; the owner did not do a good job flushing the boat and making sure the exhaust manifolds were clear of most the water when not in use. Also, go back under the motor cover and look at where the exhaust manifolds mount to the engine. There will be bleeding from those connections. If there is a lot of rust and corrosion there, beware.
Get a compression check on the engine. You are dropping serious dough on this. Wakeboarders are notorious for hammering the throttle.
Finally, just use common sense. From tip to tail there are a lot of signs that will guide you to how the owners took care of the vessel. Look everywhere and be picky. Boats are huge holes you throw money into. Even if you get the boat of your dreams, you will be fixing a boat (new or used) throughout most of your ownership.
Enjoy and I hope this helps. Todd
my blog: http://thirdcoastyachtsales.blogspot.com/