Hmmm... I'm partial to Whiterun as it was the first big city and the nicest looking one too with a cheap house that is close to the main gate and close to a blacksmith and other shops. It's also kind of centrally located and I use it as a hub for my travels.
Now, house wise, I like Markarths house because it is big, has lots of storage, good seet of bookshelves, close to the main gate, enchanting and alchemey tables as well as a display stand and cases.
I like Riften and the house too because it's close to shops, and is the only one that you can access from outside of the city. It's pretty limited on storage and bookshelves though.
As for Solitude, I like the city as it's got the feel of long time permanentcy and lots of vendors. OH to the person looking for the blacksmith, he's up a ramp across from the vendors with stalls, next to the Fletcher.
Oh and there's something that the other towns don't have, a Fletcher. That was cool.
The house in Solitude is lacking in my opinion. I should have more bookshelves and storage on all levels. Especially down in the basement where the tables are. The sword rack is tucked into a little alcove that I completely missed the first few times in there because it blended in with the wall colors. I like the two dummies though. lol. One thing I don't like is the house seems to be full of "holes". I've placed items on shelves only to find they've jumped off later and gone missing. Usually when items jump they don't go to far. These however, just fall into the floor or behind cabinets. I've had to use the console to go noclip to find and get them back.
I've seen the house in Winterhelm and it looks huge, but since I haven't picked a side in the civil war, I haven't been offered it yet and there's all the... er... SPOILER stuf there.
So, overall I'd have to say the best house is Markarth, best city is Solitude with Whiterun a close contender.