It all depends on what you are looking for.
Here's a basic rundown.
Falkreath - Lakeview Manor
Middle of a pine forest, lake in the backyard. Fantastic view of the forest and lake and distant mountains from the tower wings. However, frequent bandit attacks, pesky wolves, the occasional giant who likes to take a load off and lean on the side of your house, and a persistent conjurer who stakes out at an altar in between your house and the lake.
Personally, I like this one best. I love living in a thick, dense forest, and I don't mind the attacks. My steward will help me mop them up quickly when they do show up. I love the view from the towers, also. Damn gorgeous.
Hjaalmarch - Winstad Manor
On the northern shore of the hold, about right on the border where swamp meets snow. Has a commanding view of Solitude and all of its glory, but other than that, no other great visual aspects. Not too sure on the attacks here, as I have not spent much time at this home. If anyone else has any info, go right ahead. This house is very nice if you are really into alchemy. It has the special option of building a fish hatchery, which provides some nice ingredients, and if you combine that with the Greenhouse wing and the outdoor garden, you're set for life. I wouldn't set up alchemy shop anywhere different.
The Pale - Heljarchen Hall
On a snowy hill bordering the Whiterun hold. Has a clear, direct view of the entire plains, and Whiterun rising up on top of the hill. Love this view so much, I can't get over how awesome Whiterun looks at a distance. Attacks on this one are basically just the passive giant hanging out, since there is a nearby giant camp, so with the near absence of hostile attacks, this makes a perfect 'family home'.
This is a very close second because of the spectacular view of Whiterun from your damn front door. And, it's a safe (ish) place to keep the family if you are tired of being cooped up in those crowded cities.
That's the three homes from my perspective. They are all fantastic locations, it just depends if you are all about the looks, or don't give a rat's ass about looks and just want a safe house for the kids, or want a perfect place to brew up those noxious concoctions of yours that the neighbors were complaining about.