A lot depends on why you bought the house. Are you buying more as a home or as an investment? There is a difference.
For the most part, upgrades are highly profitable items for builders. They are not designed to increase the value of the home, but they will make you happier with the home you buy.
If you're treating your home as an investment, you'll buy smaller to mid-size on site and spend only a minimal amount on upgrades. If you are treating your purchase as a home, you choose upgrades that will improve your quality of life.
A rule of thumb is to always upgrade the carpet and padding.