A lot depends on how long you see yourself in this home, as other posters have mentioned.
One tip for any home: frequently stop by to check on progress in person and for walk-throughs (including when the inspectors are present). Whenever you can, bring your agent with you (or someone independent who is knowledgeable about the construction process). Your builder will start to hate you for it, but it keeps them honest. This is especially true if you're getting a cookie-cutter home in a planned neighborhood where their primary goal is speed rather than quality. In a custom home scenario, you're going to be heavily involved no matter what and quality becomes more of a priority for the builder.
If this is your "forever" home, then you need to be thinking just as much about 30 years down the road as you are about 5 years. In that case:
-Don't skimp on windows and doors. High quality windows (both frames and glass) help with energy costs, sound isolation from the outside world, and they can last for decades with proper maintenance. Same goes for doors. Doors and basement windows are also the primary sites for break-ins and high quality doors can deter (but never prevent entirely) criminals. A quality front door also increases curb appeal and resale. For interior doors, spend extra and get the solid-core doors. Aside from feeling more substantial and making your home appear more expensive, they also help with sound insulation.
-Remember that pipes, shower valves, and so forth won't last forever. Make sure you have some way to access this plumbing for later replacement without the need to tear your entire home apart. An access door in the back of a closet is often possible in most layouts. PVC drain pipes, if properly installed, should last forever. Copper supply lines should last 50+ years, but that will depend a lot on your water composition (water pH of <6.5 will cause accelerated corrosion of copper and pinhole leaks). If you use PEX for supply lines, it hasn't been around long enough (1960s in Europe, 1980s in US) to know it's true longevity. Most manufacturers say 50+ years, but it will depend again on your water pressure/composition, the quality of the PEX, and the installation. PEX is easier for the installer (and cheaper than copper), so plumbers tend to prefer it. There is still no definitive data on PEX leeching MTBE and VOCs into water and if it is exposed to UV light for even short periods of time (think a few days), it can lose its resistance to chlorine and be prone to rupture over time. Personally, I would still recommend a copper main line with copper supply to potable water and showers/baths just in case the PEX does leech. You can use copper-to-PEX manifolds for other applications.
-If you are in a colder climate, consider PEX-based radiant floor heat in all bathrooms, your basement floor, and in any rooms with tile flooring. It won't necessarily heat your entire house, but it does make those floors comfortable to walk on with bare feet and can help keep your home at a more steady temperature with a forced-air furnace as the primary heating mechanism.
-I can't stress this enough: make sure your bathroom is adequately ventilated and waterproofed, especially in a more humid climate like Iowa. In some areas, bathroom fan ventilation into the attic is code (which, in my opinion, is borderline criminal). Insist that all bathroom fans are ventilated through the roof and I highly recommend installing one of the new fans with moisture-sensing capabilities since the majority of people forget/refuse to turn on the bathroom fan. When the bathroom hits a certain humidity level, the fan automatically turns on and runs for a pre-set period of time. In the long run, this is going to prevent mold from setting up in your bathroom drywall. Even moisture resistant drywall is no match for a constant high-humidity environment. For the showers, make sure that there is an adequate moisture barrier around the enclosure. The older guys will use a plastic sheet behind the studs. In my opinion, this is not preferred. Some guys will even forgo a plastic sheet and just tile directly over cement board, claiming that the tile/grout with sealer is waterproof. This is incorrect as all tile is, to some extent, porous and sealer does not totally prevent water and water vapor penetration. Kerdiboard is acceptable in the right hands and cement board with either a Kerdiband or liquid membrane coating is also acceptable. In those cases, they should not use a plastic vapor barrier behind the studs - this creates a "sandwich" where any moisture that gets into the wall cannot get out and your studs will start to rot. You'd think that all contractors and builders do things "right", but they don't.
-In regions like Iowa where radon levels can be high, I would recommend installing a radon mitigation system under the basement slab prior to pouring it. It is much more difficult (and costly) to do after the fact. When your home is complete, have your radon levels tested. If they are high, then finish installing the ventilation portion of the system. If they aren't retest every few years and install one if/when needed.
-Make sure you are getting quality warranty terms from your builder on structure and installation of roof, windows, plumbing, etc. Things can and will go wrong, sometimes more than a year or two after the fact. Make them fix what they did wrong and don't pay for it.
-If you opt for upgrades, do it in the kitchen, master bathroom, master bedroom, and remaining bathrooms (in that order). Those are the rooms that will be used most often and be most prone to wear and tear.
-You can never have too many outlets.
-You can never have too much lighting.
-If you're going to run Cat5e/Cat6, coaxial, or other data cables through the home (which I highly recommend for future-proofing), then insist that they be run through a decent sized conduit. If the day comes where you want to upgrade to whole-home fiber optic or some new wired technology, conduit will make it absolutely painless to remove old cables and run new cables through existing construction. The conduit will also help to protect any expensive cables from blind nailing or other potential hazards. While the 802.11ac routers with multiple antennae can reach 1+ Gbit speeds, the potential health concerns with wireless technologies combined with fiber optic speed potential far outpacing anything wireless (fiber optic cables reaching 200+ terabit per second speeds exist but are still cost-prohibitive) mean that wired technology isn't going anywhere.
-In that same vein, having a central media area somewhere near the center of the home is a great idea. Bring in your outside cable/satellite/internet connections to that central hub and include a high quality surge protector at this central location (as well as surge protectors at individual high-cost electrical components) for coaxial and Cat5e/6 connections. Put your splitters, modem, router, etc. in that central location. If you're fairly tech savvy, you can also put a central media server here for storage digital music, movies, and so forth that can then be hard wired and wirelessly available to the rest of the home.
-My most important tip: there is a tendency for people to lean towards a bigger home with fewer upgrades rather than a smaller home with more upgrades at a given price point. I highly recommend that you go with a smaller home with higher quality materials. In the long run, it's going to save you a lot of money in replacement costs, energy costs, and will still likely be far more space than you really need.