I'm not sure what I'm repeating but here's my list:

1. Copper water piping inside the house (I don't like the plastic stuff).
2. If you're putting in a basement make sure the bottom of the floor joists are minimum of nine feet from the finished concrete (allows for a dropped ceiling so you can always add more wiring and whatever later easily).
3. Rough a bathroom in the basement (if you're getting a basement).
4. Put a conduit in that runs from the basement to the attic (about a 2"). That way you can alway run cabling anywhere in the house.
5. Add gas stubouts on your deck or patio for a natural gas grill.
6. Make sure the condensing units are more oversized than undersized.
7. Pick a location in the basement for a communications closet and homerun a cat5, RG6 and telephone cable from each room to there.
8. Insist that the builder make sure everything is SQUARE you may want to check this yourself. It looks funny when you put in tile or wood floor with wallls that are not square.
9. Make sure the french drain along the footing of the house gets put in (usually black pipe with gravel on top) so your basement doesn't get flooded. And make sure you can see either end before signing off on the house so you know where they come out. Of course if you're in Florida you won't have a basement.
10. Washer, Dryer, Refrigerator and garage door opener typically is not included in a new house.
11. Make sure you get double insulated windows (I think this is standard now).
12. If you want any landscaping lights or receptacles out in the bushes (for Christmas lights) you may want to do this.
13. Irrigation system? I put mine in myself but swear that I will never do it again.
14. Sleeve the driveway and sidewalks (for future wiring or irrigation). I put a 4" pvc under the driveway slap nearest the house as well as a 2" under the sidewalk.
15. Electronic, programable thermostats are nice but you can always add those later.
16. If you want any recess can lights instead of those builder grade fixtures, you may want to consider them throwing those in.
17. Alarm system? If you're not putting one in now maybe a prewire?
18. Think about how your furniture is going to layout and maybe even draw a picture to scale including furniture so you know exactly how to set up your surround sound system. And of course prewire it.
19. Make sure the builder will come back after a year for another walkthrough to fix any sheetrock nails that are popping out or cracked drywall or any other miscellaneous problems.
20. Make sure the sub-floor is 3/4" PLYWOOD glued and screwed to the floor joists. I'm sure you don't want squeaks and the plywood facilitates the installation of nail down 3/4" wood floors if you choose to do that now or later.

Good Luck