Apart from what all the other posts have suggested:
First, take a small tape recorder with you and use it to comment on everything you notice and check. It is easier to sit down later and write out the results using the recorder, rather than taking notes during the walk-thru. It also helps you record what the builder's agent said during the inspection.
Buy a plug-in circuit tester for about $5. It will show you not only if the outlet is live, it will show you if the line is reversed or if there is an open ground! Check EVERY outlet.
Take a cigarette (or a few joss sticks) and check outer doors and windows for draughts. Dependent on the type of HVAC systen you have, you may be able to create a small over pressure, you can also check for leakage to the outside. Those leaks will cost you big $ over the years and they are easy to fix – especially when the builder does it for you.
Not only take a level with you but also a framing square to check for correct 90 degree angle in corners – most will not be.
I paid for an external infrared check of one house I bought, to check if the insulation had been installed correctly throughout the house. Check-out the Yellow Pages and ask for a price.
Open a few taps (4), upstairs and down – leave them running and flush one of the toilets and see if the pressure drops to any significant extent – if so, demand a pressure test on the supply.
Buy a thermometer and see how hot the water gets at the kitchen sink. Then, run the hot water in the bathrooms for about ten minutes, leave them running while you recheck how hot the water is at the kitchen tap.
Take a hose and run enough water on the roof to see if the gutters leak and the run-off is sufficiently far away from the outside walls and drains/flows away easily.
IF YOU DO YOUR JOB PROPERLY, the builder's rep will become pissed-off and make some kind of fuss, but it's your money that's paying for this house – and his salary too. Ask him this: "If you've built me the house you described when I agreed to pay you $xxx for it, I am going to spend the time to make damned sure it's the house we agreed on. Just like your boss is going to make damned sure that he gets my money!"
A house purchase is usually the most significant purchase and financial obligation people get involved in. You're intitled to be an asshole when you check it out – in fact, on this ocassion, you owe it to yourself to act like an asshole!
Good luck!