There always seem to be some upgrades and enhancements that can be added to your list that the builder may not offer you because, although they may be available, the builder does not have them as standard, pre-priced options. The most common items I can think of that get overlooked by buyers and design center personnel alike are items that aren't visually evident in the home. A biggie is insulation. Ask your builder about the thickness of the insulation they use in walls and between floors. If noisy living areas are not far from bedrooms, you may want to inquire about upgraded insulation to muffle the sound.
Insulation is also important to energy efficiency.
These are builder preparations for systems you intend to install later on. Pre-wires are for electrical enhancements for later on. An extra garage door opener, speaker wire in your family room ceiling, an intercom, or a security system. A larger fireplace, more burners on the cook top, extra cabinets in the laundry room, more fans in bathroom areas, more security lights in the backyard, and even an outlet for Christmas lights in a place you don't have to risk life and limb to get to, for instance. What happens, all too often, however, is that by the time a buyer thinks of adding them, it's too late in the construction process.