For this post I'm going to deal with a fictional, open world sandbox environment.
Firstly, I think the ideal system would allow for a base house (of various floorplans and styles) that allows expansions. You would have your standard house and manor types, and each could be added on with functions that are both cosmetic and helpful. These additions would come through the player economy, via blueprints bought and assembled by characters who specialized in crafting. Decorations for the house would also be made in a similar fashion. This house would take up a space in the real game world, much like in Star Wars Galaxies, and have no part of it be instanced.
Benefits would include a rested bonus for logging off in your house, additional storage space for items, and possibly a stable of some sort to display acquired mounts.
Second is the possibility of renting out a house. By setting a house up for Rent, you can put a low daily/weekly fee on the house and allow another player to move in. This player cannot make any changes to the house, but can use it and its benefits freely. The tenet can be removed with a three to five day notice if needed, and if two payments have passed (which are automatically deducted from his money) his key to the house dissapears and all of his belongings mailed back to him. Now, this option is automatically enabled for players who have not logged in for two months. Their houses are automatically put up for rent, with the payments being deposited for them automatically, at which time they can come back and reclaim the house if needed. Players with deleted characters will have their properties set for sale at market price.
Houses can also hold storefronts, in which a clerk is "hired" for a small fee to sell your goods. There would be no Auction House, only stores such as this and marketplaces where stalls can be bought and have hired help sell your goods. You set the prices, as well as stock the inventory and decorate the shop as you please.
Enough houses in an area can give rise to towns or cities, where enterprising guilds or simply the townsfolk can chip in to create a town hall, where a leader can be elected for various functions. But player run cities is not the focus of this post, so I'll stop there.