Lakeview Manor is the best by far. In my opinion anyways. Plus the kids seem to like it the best.

Winstad Manor - I love being able to customize the house, the fishery is great, and it's close to Solitude for Merchants.

Breezehome is sort of a nostalgic favorite, since it's the cheapest and has many merchants around it, but I've always disliked how cramped it feels and how there are gaps between the wood planking, etc. The lack of enchanting table would be a killer for me, but luckily I'm on PC and have a mod to add one in.

Hjerim is probably my favorite layout and storage -wise, but has the downside of being in Windhelm, which (after Markarth) is my least favorite city, so I rarely ever live there. Sometimes I'll use it to display my trophies and such, and visit them from time to time, but I've never settled there permanently.