Make your changes on paper. Change orders after construction has started costs you more money. (Actually, we learned this from Dream House and other home shows.) We did make some changes in a bathroom, but that was because someone changed her mind. And we caught the kitchen window in time--on paper.
Make decisions about upgrades early. I'm sorry we didn't spring for the new doorbell and have the builder's electricians install it. We'll do the sound box some day. Retro fixes are expensive, but sometimes you have to wait. Think about it. Something to pay more for is noise insulation. It's really important between a bathroom and bedroom. Sometimes what you want is cheaper than what the builder was planning to install. We went for the faux marble windowsills instead of wood in my mother's house. I never want to paint or repair rotting wood again.
A big and necessary expense nowadays is wiring for computers, phones, cable, a speaker in every room, an alarm system, possibly even a smart house. What about a central vaccuum cleaner? Do you need one? This, along with style and an elegant facade; an impressive entryway; Corian, granite, or marble counters; high end appliances; a fireplace; a swimming pool; an exercise/game/home theatre room; a bathroom for every bedroom; an outdoor jacuzzi; high and fancy ceilings; skylights; etc. is where you think hard about priorities. Some people build a smaller home so that they can spend more on quality. Your decision, but be sure you have enough storage.
From: Building a Cool House for Hot Times without Scorching the Pocketbook (#6 on this Barnes & Noble list): Barnes & Noble.com Books - Architecture, Domestic->Amateurs' manuals