There have been some very good threads on Houzz about must haves for custom homes so I suggest you go searching through old discussions for some great ideas

For a farm house, I would suggest an extra large mudroom, a 3/4 bath, laundry room and office space off the back door or family entrance. Filthy dirty clothes and people never get into the main part of the house. I would use tile for the bottom portion of the walls around the entry door and mudroom space. In addition, have a large closet for work clothes and coats in the mudroom and separate closet space for good coats. A kitchen sink in the mudroom or laundry room makes a good area to wash up with more space than your typical bathroom sink. One of the old fashioned kitchen sink with the built in drainboards works great for this.

One of the challenges of living on a farm is keeping farm dirt from getting into the main portion of the house. I suggest having enough space for all the farm business and visitors, the work clothes and the dirt in the back part. Build an office with a door which can be locked if needed; if you have someone stay in your house while you are gone elsewhere, you may want to keep your business area private. Likewise, it might make sense to have a physical door between the back area and the main part of the house so you could lock your home and still leave access to the business/work zone.

Another area of concern is weather...many farm houses aren't very sheltered. Consider using hurricane straps for the roof and anchor bolts for the sill plates to help survive wind storms. If you don't have a basement, build in a shelter room, perhaps the work area 3/4 bath or your office and install a solid door to the space.