These are some cool ideas I've had that should be easier to do if you do when you're building a house, rather than having to remodel.

• Intercom with radio/cd
• Network every room, preferably with CAT-6 STP cable
• 20 AMP electrical circuits everywhere
• Solar power
• Secret passages/doors
• Alarm system
• Built-in/anchored safe
• A/C zoning
• Ultraviolet A/C filter
• Poured-in-place exterior walls, or cinder block with rebar and concrete poured in the holes
• Door handles instead of knobs
• Handicap width hallways, doors, and entrances
• Pocket doors, potential use: sound zones
• Extra long soffit-vent overhangs over windows
• Rain gutters
• Double-paned and/or impact resistant windows
• Mini-blinds between glass panes
• Water softener/filter
• Lawn sprinkler system
• Central vacuum
• Dog door
• Solar screens
• Dumb waiter
• Blower on a gas fireplace
• Instant water heater
• Gable/tray/layered/slanted ceiling
• Personal water well
• Spinning TV cabinet to hide the TV as a bookshelf
• Extra wide door border (to go with crown molding)
• Fire pit in the pool
• Pneumatic tubes to each room, like the bank drive-thru
• Model trains that run through along the crown molding from room to room and through holes in the wall to skip the doorways
• Drawers in the staircase
• Panic room
• Corridors inside key walls (wiring, sound proofing, secret passage, storage...)