Honeyside, in Riften. Nice and cozy, and has a fully stocked alchemy and enchantment room. The smithy is pretty close, too, much closer than dragonsreach enchantment table to breezehome. The only strange thing is that if you get married your spouse doesn't sleep in the main bedroom, they sleep on a random pallet in the basement :P
Proudspire Manor is where I have all of my stuff...it's fully furnished although I never use the second floor for anything as the Thane's Suite is on the third floor, and the first floor is where the Alchemy Lab and Enchanting Table are. I own Honeyside, & Breezehome in Whiterun as well. I still keep all of my smithing supplies at Breezehome. It's small but functional except for no enchanting table and right next door to Warmaiden's. Although not a "home" the Arch-Mage's Quarters is a nice place to call home too.
I got the Breezehome only because I could afford it at the time. It is in a good location (although really it doesn't matter since we all fast travel alot). But I do like how I spawn pretty much right by my front door. At first I was storing all my stuff at Jorraska (took me awhile to figure that out, thank god) then decide once I got the cash went for the cheapest, Breezehome. It's funny, cause I almost want to buy another home. Have the coin for it-money's flow in well now and I'm not buying anything unless I spend on training. There's some glitch I think on the "weapons rack" in Breezehome. You can't "activate" it. That kinda blows.