I could write pages. But instead I'll be brief. I'm in the process of having a home built from scratch, on a lot we bought on our own.
Here's how it can break down:
Option 1) Be your own general contractor
It's basically a full time job, you pick out all your subs, do all planning, apply for all permits, and generally have to project manage the thing start to finish. You might save $50k-$100k. You might not. You will have a nightmare and a huge time hole, doubly so if you have a complex home and have no prior building experience.
Option 2) Go with a builder that will GC for you
Which leads to more options...
Option A) No custom at all short of maybe flooring and counters. You get a house completely designed with no flexibility in arrangement/size by the builder. You walk in and they sell you a house they want to build.
Option B) Psuedo-custom. The builder has a set of general plans that he likes to use that you can make bigger smaller/and flip around things like doors, windows, siding, garage sizes ect. And you typically have full control over your allowances. You walk in, they ask you a price range you are looking at, and then show you some options and ask you what want to change about the plans.
Option C) Full customization. You walk in and they ask "What kind of a house do you want us to build you?". You can either take in a plan you like and they'll draw one up based on it, or you can sit down with the architect and you guys can slave away on every little detail until it's YOUR home.
....
We looked at all three builders and settled on option "B". The builder had a very good idea of costs almost down to the board on what it would be to build the homes we were looking at. We also had the ability to change up room sizes, layouts, ect without having to sweat every little detail. We were turned off by the first type that didn't even listen to what we wanted, and too overwhelmed (mentally & financially) by the full custom option.
If you are currently a home owner, building is not easy. Many banks will require your home to be sold or solid offer on it before you can get going with the construction process. And since the construction process is typically 4 months to over a year depending on the home staying in your current place just isn't feasible.
If you are renting it's not too hard.
Probably the hardest thing to do is stay within budget. There are just so many places that you can get out of hand. I budgeted for $20,000 for a well & septic system (no public water where I am). My $10,000 well turned into over $25,000 when I couldn't get water going shallow bore. So I just blew that budget by over $10,000 when you factor in the cost of drilling the well and adding in an RO system to make the water drinkable.
Same with flooring. Your builder might give you a $7,000 flooring allowance. We actually had $12,000. Which sounds like a lot. But we had over 3200 sq/ft to cover. That's $3.75 a sq/ft. Cheap hardwood is $3-$4 a square foot. Plus another $2 a sq/ft for installation. Tile installation is even more. Carpet can vary wildly by price and quality. It's just very hard to keep on track with that stuff, especially if you aren't going to do any work yourself.
The thing I can not empasize enough is DO YOUR HOMEWORK!!! Ask around about the builder, check his BBB rating, ask for piles of references, ect. If you guy by the cheapest you are likely going to get burned. Go by the best referred. Our builder did houses for 5 coworkers of my wife and every one of them was very satisfied with the quality, value, and construction process of their home. He also has an exceptional reputation around the area. He also is nationally recognized for his energy efficieny and construction methods in his homes. So that was a plus too.
Which is my second next point...the advantage of going custom/pseudo custom is you can control your efficiency of your home better. Insulate and seal as best as you can and save on your bills without any fancy or expensive alternative energy methods. Just simply build a good home!
Which is another point...you probably aren't going to keep the place forever...don't get too cheeky with it. Unique tastes in homes take unique tastes to buy them. Many people don't take risks on such big purchases. Be mindful of any crazy options/upgrades/designs you do. It might cost you bigtime down the road.