I prefer the Whiterun house because it is a nice central location to the whole of Skyrim, has smithing and smelting facilities right next door, has archery ammo store across the street, and has alchemy and enchanting ( with the mod that adds an enchanting table to it) in the home. Also very quick access to stores for selling of any type of goods within very short running distance.
It may be the least fancy of the houses, but it's the only one that has all of the above going for it.
So far I have acquired 2 houses: the one in Whiterun and the one in Markarth. Markarth is 8,000 gold and is really spacious and nice once decorated. If you like lots of books, it has a library with 4 book shelves.
I prefer Proudspire Manor in Solitude now I've modded it a bit. Fast travel to Blue Palace, quick sprint and you're at the back door.
For such a large house, it doesn't have a lot of weapon racks or enough bookcases.
I've knocked some walls out in the basement and added a complete smithy down there, even Ysolda goes down and uses everything. I've added some display cases too for jewels, rings, masks etc, I did add a nice table too with all the bits on but Ysolda can't work out her way around to the Arcane table so she walks over the top and knocks it all off. Skank.
I still have a soft spot for the house in Riften though, even though I've got a serious butchdyke haunting the place. Sitting on the verandah, shooting fish.