A lot of it depends on how long you're planning on being in the house. If you're going to resell any time soon, keep an eye on putting stuff in that will help resale value without doing anything too over the top that you won't get money back on (or may be too specific to appeal to buyers, like pink marble countertops).
We just finished building, so I'll toss in a few things:
Carpet: I don't remember a lot about this, but the pad quality makes a lot of difference in comfort and wear.
Flooring: Everything has its drawbacks. I've had engineered hardwoods before and didn't like the look or feel. I've had real hardwoods and hated it when they got fucked up. I've had wood-look tile in a rental and hated the feel and grime accumulation in the grout. We went with stained and scored concrete this time, but it's so highly variable in how it turns out that it made my wife apoplectic at several points. One thing we almost did was the new wood-look vinyl planks. Sounds cheap and shitty (and some is), but some of it looks really good, and it's supposed to be very durable and repairable, especially if you have dogs.
Countertops: I wanted to try soapstone, but nobody around here had much experience with it. We went with granite. Pricing goes up with grade (essentially the pattern, I think), and thickness. Don't get a dated edge like bullnose. The new engineered quartz stuff is popular, but was too modern for us, and it can get as expensive as granite.
Cabinets: your wife will tell you what you want. Do deep, heavy duty drawers for heavy/bulky pots and pans.
After we were done, the trivial things that pleased the shit out of me the most were:
-- Heated floors in the master bathroom/shower. Really not that expensive to do before the tile goes down, really expensive to go back and do later. Protip: don't forget the shower bench.
-- Trash drawers errywhere. Put one anywhere you might do food prep. It's so nice not to have to drip messy shit all over the kitchen floor trying to get to the one trash can you stuck in the pantry as an afterthought.
-- Don't forget to add electrical outlets by the terlits for Surly 1% bidets.
-- Solid core master bedroom door. Keeps noise from the kids out, noise from your mom in.