What should I look for during a deficiency walkthrough?
At the risk of simply stealing something from the internet and re-posting it (oh the horror!)...

http://coolthingstoremember.blogspot.com/2006/09/new-home-walk-through-checklist.html


  Pre-Delivery Checklist
  
  Bring a level, measuring tape, notepad/pen, flashlight, mirror,
  stud-finder …
  
  Doors
  
  
  Open and close all doors. See that doors are well-fitted and operate as intended.
  Make sure all six sides are painted – front, back, top, bottom and both ends.
  Be certain locks, including deadbolts, operate properly without binding, and that thresholds are adjusted correctly.
  Look for warping.
  Hinges should be clean and free of paint.
  Sometimes doors must be trimmed to fit. Make sure the cut is at the bottom, that it's straight, and that so much hasn't been cut off that
  the door is now hollow at the bottom.
  Check that locks are well-installed and do not rattle when the door is closed.
  Check that the exterior doors have been sealed with weather-stripping.
  
  
  Windows
  
  
  Open all windows.
  Determine that locks operate properly.
  Tracks should be lubricated to prevent binding.
  Make sure screens are in place and not torn.
  Look for broken panes.
  
  
  Walls
  
  
  Walk the perimeter of each room, checking floor and ceiling moldings to be sure they are uniform.
  Look for gaps that need caulking, protruding nail heads and proper finish.
  Examine all wall and ceiling surfaces under natural light and, if possible, at night under artificial illumination. Poor drywall work
  tends to show most when the lights are on.
  Look for visible seams, nail heads that have popped out and other irregularities.
  Be sure the walls are square. Otherwise, the tile floor or patterned vinyl floor will be askew. In such a small space, anything
  that's out of line will become a constant source of irritation.
  Inspect the wall finishes for uneven paint coverage.
  
  
  Electrical
  
  
  Be sure all wall outlets and switches operate correctly.
  Test light fixtures, making certain they are attached securely and contain the correct-wattage bulbs.
  Locate the main electrical panel and review the function of each circuit breaker and fuse.
  Your new home must be equipped with ground fault and arc fault circuit interrupters (GFCI and AFCI). GFCIs protect bathroom and
  exterior receptacle circuits, while AFCIs protect bedroom receptacle
  circuits. Ask your builder how to test these devices.
  
  
  Flooring
  
  
  Tile and vinyl flooring should be clean and free of chips and cracks.
  Check for missing grout, and be sure molding is installed and painted or stained.
  Walk all carpeted areas, checking for loose fits at the edges, ripples in the middle and squeaks in the subfloor.
  Walk across all floors. You should hear only a minimum of squeaks and notice a minimum of spring when walking on the floor. Due to the
  nature of wood, a wood floor system will have a certain amount of
  unevenness.
  See that floor coverings have a relatively flat surface.
  Examine seams in carpets and vinyl to ensure they are tight.
  Inspect ceramic tiles for surface cracks. Joints between ceramic tiles should be well-filled with grout.
  Inspect flooring for damage.
  Examine carpeting for stains or shade variations.
  
  
  Kitchen
  
  
  Check countertops for scratches and abrasions, a frequent complaint. Counters are a magnet for toolboxes from every trade.
  Also make sure the cabinets and appliances are level and properly anchored to the wall or secured to the countertops.
  Check all doors and drawers. They should open fully and without binding.
  Ask for the instruction manuals for every appliance in the house – the range, refrigerator, dishwasher, furnace, heat pump, water heater,
  electronic thermostat, everything.
  
  
  Bathrooms
  
  
  Look for scratches and nicks in the sink as well as the shower enclosure and tub. Workmen like to put their toolboxes there as well.
  Check that the sink and tub stoppers hold water, and that the shower strainer is fastened securely.
  Make certain the toilet is securely fastened to the floor. Don't test the commode by trying to rock the fixture back and forth. That
  will break a seal that's correctly installed. Just sitting on it is
  enough to tell if it is tight.
  While sitting there, close the door and take a long, hard look at the walls and other surfaces to make sure they are acceptable. Flaws
  show up most when semi-gloss paint is used, and that's what bathrooms
  should be painted with, not flat paint.
  While you're at it, be sure to see if the toilet-paper dispenser is at the right distance and height. If it isn't, you may have to be a
  contortionist to reach the roll.
  Check for chips in bathtubs, toilets and sinks.
  Ensure that all faucets work properly.
  Check that cabinets are securely fixed to the wall.
  Examine caulking around tub and shower enclosures and at countertop backsplashes.
  
  
  Heating/Air-conditioning
  
  
  Test for cold A/C.
  Check the furnace and hot water heater.
  Ask about the capacity, shut-off mechanisms and the type of filtering systems installed.
  Review the operation of your heating system.
  Locate the furnace filters and ask about their care and maintenance.
  Ensure that heat registers are not located below a thermostat.
  Check the location and number of cold air returns and make sure they are unobstructed.
  Learn the location of any fuel lines (gas, propane or oil) and understand how to operate any shut-off devices on these lines.
  
  
  Mechanical ventilation
  
  
  Locate the switches for ventilation and circulation fans (normally placed near the thermostat).
  Locate supplemental fans and switches in each bathroom and in the kitchen and ensure they are operating. Make sure you understand how to
  achieve proper ventilation in order to avoid condensation problems
  which may not be covered under the warranty.
  
  
  Plumbing
  
  
  Locate the shut-off valves for the main water supply and the location of other shut-off valves throughout your home.
  
  
  Kitchen
  
  
  Check for damage to countertops, cupboard doors, sinks and appliances.
  Ensure that cabinet doors are properly aligned.
  Check spaces for standard appliances unless specific measurements were given to your builder. The space allotted for your appliances
  should be correct.
  Test the range hood fan and light.
  Make sure there are electrical outlets above the counter.
  
  
  Closets
  
  
  Make sure that doors are secure and that they open and close easily.
  
  
  Upgrades and options
  
  
  Rain glass it kitchen cupboards.
  Rain glass shower enclosures.
  Tile in kitchen and bathrooms.
  Vinyl in laundry.
  Marble in bathrooms.
  Granite in kitchen.
  Correct carpet and pad.
  


That list is pretty comprehensive. :)