No 1st hand experience, but my friends that have done so. Some of it is common sense, but there are some things that I didn't think about. They tell me to make sure you are pretty specific in how you want pretty much everything, even the little things that you don't think are that important, such as light fixtures and switches. Even the small things can add up to either a lot of savings or a lot of cost. Also, make sure you collaborate with your contractors often so that the plans and layout are sensible for you. Some stuff is easy to change once it's done if you don't like it. But some stuff can be a pain in the ass to have to change if you don't like it when the house is finished.
We've seen a few different spec homes this builder has built recently and we like the way they look, just wanted a different floor plan, so I don't anticipate too many issues once it is finished. My wife is pretty excited to pick everything out but I'm mostly concerned with the pricing of everything.
I don't know where you live but think about the weather conditions, especially if you live in the south. If there is something you really want, it's better to put it in from the start. Don't worry so much about furnishing at first. That can get expensive fast and you can do that a little at the time, plus your ideas about that will change as you live in it a while.
If you have a 2nd floor think about a good wall fan to draw out the hot air. Even with central air sometimes you need to air out the whole house.
Think about storage space, A LOT, and put in the attic space if you can. Put in as much storage space as you possible can. You will need it.
Put in a deck if you can, and make it as bigger than you think you need.
Building a ranch, with a basement, in central Illinois
We sold our old house because of lack of space (2 kids under 5), so space, storage space particularly, is a big priority for us. Definitely planning on putting some plywood down in the attic in the garage once the frame is up. Starting with a patio in the backyard for now, but will definitely be adding a deck in the future.