1. Make sure you and your wife are on the same page about priorities and finances. Even when it's fun and exciting, building a home is super stressful and can reveal some differences that you never knew were there. So no matter what, prioritize that connection and cooperation in both the planning and implementation phases.
2. Put your money where you can't see it. Sorry. It's not particularly fun, but it is by far the best financial choice for the long-term. This includes:
a. A good architect who knows about energy efficiency. Your biggest cost driver will be the amount of square footage. So hire an architect who can plan a smaller house that will still meet your needs -- or maybe develop a design that starts small now but has a pre-planned expansion ready to go when you add those extra kids. Clever use of space is always better than more space.
b. Energy efficiency. Spray foam insulation is absolutely worth the price, because it also works as a barrier against leaks and can get into areas that are very difficult to manage with more traditional insulation. Good-quality windows are worth the money -- but you also need to ensure they are installed properly (which a decent modern window, a lot of heat gain/loss is due to leaks/gaps around windows vs. through the windows themselves). This is also where a good architect can earn their keep, with things like large eaves in hot climates and south-facing window walls/passive solar in cold ones. Siting, orientation, and overall plan are worth their weight in gold when done properly, and can never be fixed for any amount of money when they're screwed up.
c. Quality construction for anything you want/expect to last over say 10-15 years. E.g., do not buy particleboard or MDF cabinets for anywhere they may get wet, because if they do, there's no fixing that. It's a giant PITA and huge cost suck to replace kitchen cabinets, so it's worth paying up for well-constructed drawers (e.g., dovetail joints or the modern equivalent), heavy-duty glides, 3/4" plywood construction, and the like. OTOH, it's really really easy to replace a countertop. So if your budget won't cover both good cabinets and fancy countertops, go with the good cabinets and laminate countertops.
d. Ease of maintenance. This is purely a lifestyle thing. We bought a house with vinyl siding, which I have always, always hated. 19 years later, we've had to do precisely nothing to it. OMG am I a convert now. YMMV, of course, but do pay attention to lifespan/maintenance along with cost.
e. It may be worth it to consult a landscape architect/designer if you're building from scratch. You really want to make sure that groundwater and stormwater won't settle/collect around the house, so you want to have everything sited and graded appropriately. That can also help you start to get a sense of what the property will look like in the end, so you can think about views from various locations and make sure you have windows in the right spots and plants in the right spots and all.
3. As a practical matter, take plenty of time to develop that plan and to work through the motions of daily life to figure out how you will live there. Example: when we did a huge remodel c.2006, I designed the kitchen myself, because the whole triangle workspace didn't fit with the way I cook. So I did different zones -- so for example I have my fridge right across from the island sink, with a drawer with knives and cutting boards right next to the sink, so I can do veggie wash/prep all very easily - then turn around and plop it on the stove, which is surrounded by the spatulas and pots and pans and stuff I use on the stove. The other side of the stove is a baking center and dry good storage, along with bowls/mixer/whisks, so it's equally convenient for mixing and that part of the prep. The dishwasher, OTOH, is on an entirely different leg of the kitchen, because DH does that, so he has a separate big sink for dishes next to the dishwasher, with all the dish storage right above. The more thought you put into that kind of detail up front, the better the house will suit you long-term.
4. Where you can, take advantage of periodic sales. We bought all of our appliances on Black Friday with a 30% off deal, then stored them in the garage until now.
5. Take your time choosing your builder. Any builder is used to building a certain type of house, with a certain level of finish. If you're not going to be building the standard house, you need someone who will take the time to listen and is willing to do things your way. (We're rebuilding now after a fire, and this is our third project with our guy, and he now just rolls his eyes at us when we come up with something else -- but he always makes it happen).
6. Splurge on a couple of things that are really special to you, and go lower-end on everything else. Don't get sucked up into the idea that everything in the house needs to be at the same cost level (which is what will happen if you go to like a kitchen designer or something). Really, Home Depot/Costco/scratch-and-dent stores/recycle shops are just fine for 95% of things -- particularly for things like appliances, which have a limited shelf life anyway. So build your choices around those options. But at some point, you're going to feel like you're spending all this money, and yet you're not getting anything that you actually really want, because you're compromising on everything (at least, if you're like me you will). That's the point at which it's very helpful to say, "dammit, I really want those real wood floors, even if they are $1 more per square foot, and that's where I'm going to splurge."