I have a section in the middle of my town with two of each house surrounded by brown houses. It is directly under where the game opens up to if you are visiting. It lets people visiting get in and out fast if all they wanted to do was farm.
Surrounding that is my nicer bits of town. I organized into sections of shops and municipal buildings with a more natural neighborhood with the significant houses in it. I also have an industrial complex. I spattered the restaurants and whatnot around the shops and municipal buildings.
Then way off to one side is a blue house farm. It currently generates enough income for 2-3 chunks of land a week, which covers big updates like this one. But soon it will be slower than that and I will need to add more houses. I think the trick with house farms is to keep them way off to one side and just pretend like they don't exist.
I also regularly restructure my town. the center of the town shifts when you buy enough land, so I move "visitor village" back to the center and move new buildings around into their proper sections of town. Right now the edges look messy where I have put all the new buildings, but when the update is over, Ill move the mapple store to the shopping area, the hospital to the municipal zone, etc...