All the suggestions posted on this thread have been so valuable, though I'm sure many of you (like myself) find your head spinning with all the ideas, so I just sat down and categorized them all!

Closet & Organization
- Plugs in several closets
- Make sure your closet has enough space for both double hung rods, and singles to accomadate long clothes
- Full size broom cupboard in pantry or laundry room to hide all the cleaning items away from sight.
- More closet/linen space than you think you'll need
- Cubbies in mudroom with an outlet in each one
- Motion sensor on pantry and closet lights

Bath
- Plug in master toilet closet for night light
- Outlets inside vanity cabinets (upper and lower) in bathroom for dryer etc.
- Heated towels racks
- Don't caulk the bottom of your toilet to the tile to hide potential leaks
- Make use of the pony wall in a bathroom by turning it into storage.
- Vac pans for hair
- Appliance garage on counter

Outdoor
- Run conduit under the driveway for future wiring or plumbing needs
- Prewire speakers both indoor and outdoor
- Ensure you have hose outlets and power on all 4 sides of your house, and on top of any raised areas
- Hot/cold outdoor water is good for washing pets
- Motion sensor pre-wire for selected exterior lights
- Keypad entry on garage door (Keypad entry on front door is great as well)
- Gas line to grill

Kitchen
- Plugs in kitchen pantry for charging, or for items that may end up living there
- Recess the fridge
- With wide islands put cabinets on the both sides. While they are not easy to get to, they are good for storing seldomly used items.
- Built in paper towel holder
- Custom storage organization in kitchen drawers
- Warming drawer in dining room
- Pantry entrance near both kitchen and garage
- Custom shelves and a place to plug in appliances in pantry
- Plugs above cabinets for Christmas lighting
- Set up for both gas and electric appliances
- Pantry door on swivel
- Pantry light on motion sensor
- Copper tubing for your ice maker from the freezer and until it's out of the kitchen wall
- Drawer microwave
- Knife drawer
- Pull-out garbage/recycling/laundry (for dirty dish towels/napkins/bibs!)
- Paper towel holder in drawer slot
- Drawers for all lower cabinets (more efficient use of space)
- Two soap pumps at sink (one for handsoap, one for dish soap)
- Easy-access place to store frequently used appliances
- place to hang hand towels & aprons

Electrical & Plumbing
- Prewire security system & cameras
- Run wire and prepare roof for future solar
- Run a 2" PVC pipe up from the basement to the attic for future wiring needs, some suggested double conduits.
- Seperate 20z circut with outlets at waist height in garage to plug in tools
- Seperate 20z ciructe for TV and a/v equipment
- Identify areas for low voltage can/rack
- Pre-wring for music and speakers, inside and outside
- iPad controllers in the walls to control whole house music systems
- Pre-wire for generator to essential areas
- Carbon monozide unit on the wall upstairs
- Make sure plumbing in bathrooms are done correctly. One commenter's toilet was placed too close to the tub pipes so I couldn't get the deeper tub because they didn't allow room.
- Cast iron pipes for the plumbing drops from the second floor cuts down on noise
- Take pictures of all the walls before Sheetrock went up so you knew where all the wiring was in case you needed to add or change anything.
- Include a 220V to garage (tools, future electric car etc)
- Measure the location of anything under the slab, and various utilities out in the yard.
- Run an electrical line with a few floor outlets, especially since we have very open floor plan and couch sets are not against a wall
- Plumbed for a built-in drinking fountain,

Lighting
- Light switch to the attic in the hallway (and remember lights in attic in general)
- Solar tubes in areas that don�t get natural sunlight
- In cabinet lights and outside lights on timers
- Make sure you check the cost ratings of ceiling fans
- Check all remotes for ceiling fans prior to construction completion
- 3 way switches where helpful
- Master switch from master that controls all exterior lights
- A master switch at each exit (Front, back or garage), that turns off all of the power to the switches/lights in the house, so that you can turn off all lights without going to each room and/or light switch.

Master
- 4 plug outlets near the bed in the master
- A light switch at the head of your bed so you can turn out the light once you are in bed.

Holiday
- Plugs under eaves for holiday lights, with a switch inside to turn on and off.
- Enough storage for Christmas decorations
- Seasonal closet with hangers for wreaths, and space for rubbermaid storage boxes.
- Plugs for Christmas lights: over cabinets, in stairway, in porch ceiling, under eaves

Heating, Cooling, and Vacuums
- Central Vac with vac pans, if you have hardwood floors - get a Hideahose
- Plan where furnace vents will go instead of letting the builder decide
- Hepa filtration for allegergy sufferers
- WarmFloors heating

Overall
- Read Myron Ferguson has a book out, "Better Houses, Better Living"
- Receptacles for fire extinguishers. Maybe plan some cutouts so they are flush to the wall.
- Where possible pocket doors
- Secondary dryer lint trap http://www.reversomatic.com/category/Accessories-Catalogue/Lint-Traps.html
- Soundproofing where needed
- Stairs from garage to basement
- A phone by the door leading into the garage for those pesky calls when you are getting in or out of the car
- An inside button to open and close your garage door for when guests arrive and its raining.
- Additional support during framing on the top side of windows for curtains
- Power outage flashlights and keep in outlets around around house. Recess these into the space with each fire extinguisher.
- Mailbox sensor to alert you whenever your mailbox is opened so that you're not running out of the house checking for mail when it's not there.
- Ensure builders don't "box" off spaces, where storage or shelving could go
- Make copies of manuals prior to installation and give the builder the copies so you can keep the originals.
- Minimal walls, and lots of windows.
- A laundry room. Not just a hall, or closet, a room.
- Spindles and hand rail made that can be removed for moving furniture
- Handicapped accessible.
- Plan an elevator shaft in case you want to install one later, in the meantime it will serve as storage closets.

Pets
- Plan a specific place for your dog food,
- Place for the kitty box,
- Place for dogs to be bathed
- place for dog crates
- Exhaust fan in laundry room for litterbox

Regional considerations:
- an ante-room, with coatracks and shoe storage, and a way to keep the heat in.
- An entrance to the basement from outside for salt delivery, repair men etc so they don't track thru your house.
- storm shelter to weather the threats your area faces.
- a mosquito system http://www.mistaway.com/watch-the-mistaway-video.html and http://www.mosquitonix.com/mosquitonix
- little covered niche for bear spray at/near each entry.
- Drain in the garage to get rid of the excess water quicker from vehicles after it snows
- Pest line (brand name Taexx) a small tube is run around the perimeter of the home through the framing, and then pest control can spray within it.