1. Garage Floor Drains - Not Included included in the base price of the house - it cost us about $500 for each drain we put in (we had a 3 car garage and put in 2 drains).
2. Basement Windows - if you're going to have a deck, make sure it doesn't cover up your basement windows. Our project manager made the change without charging us anything!
3. Negotiating - when we purchased our house, Ryan Homes had just gone through a pricing revision (at least that's what we were told), where they reset their prices to be the hard and fast price. This evened the playing field because previously buyers who were good at negotiating received a better price than those who were not so good negotiators. We tried to negotiate some, but we didn't get anything beside the promotions and incentives that were already provided (which were pretty decent at ~$40,000).
4. Know your Lot - your house is not allowed to look like your neighbor's house or your neighbor's neighbor's house (so houses 2 away from yours). Keep this in mind because the Elevation (what the front of your house will look like) for houses with the same floorplan and the Siding Color will need to be different, which could force you to spend extra money (i.e. our neighbors had the same floorplan and had selected the included Elevation. The next Elevation in price was one with a front porch, which we probably would have selected anyways, but cost an extra $12,000.
5. Research your Mortgage Rate - most likely, you'll sign the papers and put down a deposit ~ 1 month before digging starts. Rates can change drastically in that amount of time. Make sure you can afford your monthly payment not just at the the rate quoted in your estimate, but I'd say at least 0.5 higher. And then, if you have a goal rate in mind, ask your lending agent to quote the daily rate (when your ready to lock) AND any discount points they're offering (for example, they will quote 4.125 with -0.125 off at closing, but they also offer points that can be paid to decrease the interest rate, but you have to ask for it. Some of the sites, I followed daily that were helpful in understanding the market:
http://www.mortgagenewsdaily.com/mortgage_rates/daily.aspx
http://www.plnmortgage.com/DailyRateLockAdvisory
http://www.citycreekmortgage.com/Daily-Rate-Commentary
http://www.yourfhaguru.com