Vlindrel Hall is my favorite house in the game. It's quicker to get to and more conveniently laid out than Proudspire Manor, but still has plenty of room, and to me it just feels more like a home. Most of the others feel like a kitchen+bedroom with storage area, Vlindrel Hall feels to me more like the person living there might have friends over once in a while.

Proudspire Manor, though, just has a bad layout. It's not convenient, it's not cosy, it's just odd. If nobody already has a mod adding a forge to the basemant, I'll probably look into it once the CK comes out. Too much wasted space, and that house is expensive enough it ought to come with its own blacksmith shop.
Breezehome feels too cramped to me (I'm always knocking stuff over) in spite of it's very convenient location (Though I need to look into this business of a mod that adds an Arcane Enchanter to it... It might be worth having with one of those in it)
Honeyside is my second favorite house... It'd probably be my favorite if there was a container near the alchemy station (or had a nicer looking entrance... Front door opening directly into the kitchen just rubs me the wrong way). I haven't gotten Hjerim on any characters because so far I've refused to do the Civil War BS, but considering it's in the farthest corner of town from the main gate, I probably won't like it much anyway.