The houses I like most are the ones I'd most like to live in. More often than not, it's because the person who made it wanted to live there themselves.
For example, Korana's Ascadian Rose Cottage is based on a real cottage she's been in. I also adore Castle Vianden by ReflectioN, which is a near-replica of a real-life castle.
It doesn't
have to be real, though. Grumpy's Asgard and Korana's Pearl Palace are very much in the realms of fantasy.
What's important is that whoever made it sat down and thought about what they would want and need in a house. It goes beyond the merely functional to something genuinely homely.
For example, the player housing (quarters on the spaceship) in Mass Effect 2 is vastly better than Mass Effect. This is because in Mass Effect they clearly thought, "Hmm. They'll need quarters, so let's just stick a room with a bed and a desk in it, and that can be their quarters."
That, frankly, is just not good enough.
For Mass Effect 2, you walk into the captain's cabin and on the right is a desk with an interactive personal laptop, a photo of your loved one, a pet hamster (if you purchased one) and assorted clutter. On the left as you walk down is a giant fish tank and then by the bed is your wardrobe, a music player, and of course the bed.
Much better.
It doesn't matter that you're dealing with fiction and fantasy here, the point is that someone sat down and thought about all the things that make a difference between a house and a home and included them. You don't
have to have it all scripted to be interactive, but you
do have to be clever in any way you can. It can either cleverly blend in with its environment ... or you can cleverly stand out through use of unusually-placed statics, clever scripting, etc. etc. A great example of the former would be Vivec Redoran Condo, which neatly and cleverly fits in with what you'd expect to find in the Redoran waistworks. A great example of the latter would be Japanese House by SniperDaria, which is highly unusual for Morrowind but remains a favourite of mine because of the simple, elegant innovation of its use of everyday items from the construction set.