I looked up all the properties I can buy and houses I can build, and on the first description (Dawnstar House) I realized that it looks exactly like Lakeview Manor which is the only one that I knew about before looking all the properties up.
The three Hearthfire construction properties, with regards to the house, are identical.
However, each of the site have a single unique property:
Lakeview Manor: apiary
Windstad Manor: fish hatchery
They also have different outdoor mining spots for clay and stone.
I've always picked Windstad Manor for the fish hatchery because fishes can give you amazing potions, and it is a reliable source of salmon roe.