So the only closest thing I've seen to this is "Which city is the strongest", and I am quite curious about your opinins.
So Bruma is my favorite because it seems like a quaint, safe and out of the way place to settle down.
What's your favorite?

Skingrad, I like the layout, as well as the style. And Rosethorn Hall, and The best quest taking place there help too

Tough choices I like them all equally but I went with Skingrad. Lets see, Awesome Count, Best house, weird people in town, Guard Uniforms, Wine, Wine, and more Wine yeah its a simple choice

Unmodded I like cheydinhal for the prettiest, Bruma for the shops, and Leyawiin for the vibe and free places to live.

Modded, they are all fantastic, Bravil's a hell hole, Leyawiin is flooded plus Anvil has a fleet with a proper harbour.
I would go for Bravil however because its so shockingly good.

Chorrol, it feels more down to earth.

Anvil at sunset looks just awesome.

My favorite is the Imperial city, jewel and center of the Imperial Empire. I love its majestic, Ayleid architecture, organized design, and grandness.

Skingrad. A vampire count, an easily protected castle, cool guard uniforms, Agnet the pickled and one of the best quests ever (Whodunnit?).

I voted Chorrol. I'm not sure why I like it, I just think it's the most comfortable and cosy town. Nice people, fine buildings, and a situated not far from neither Anvil nor Imperial City - two other town I like very much.

And are there free places to live in Leyawiin?

Yes in a way if you count performing quests as free, and don't mind getting "broken into" with some, what with random respwnable hostile npc's placed there ( i.e greyland )
Just outside of Leyawiin, you've got Grayland and the knights of the stallion lodge, both have non respawnable containers but I would check which first.
Other than those the mages guild and fighters guild, are pretty decent imo, not sure about unmodded containers, but they have room to sleep at least.

Anvil has the ship, and the farm house on the western coast, the ship has a few non spawnable containers, but the farm house I am not so sure about.

I voted Skingrad, as that's where I forsee my newest character setting up shop.

Generally though, it depends on the roleplay. For example, a Morrowind native Dunmer would live in Cheydinhal. My Nord would have lived in Bruma, etc.

My elf was born and raised in Bravil. In her heart, it will always be home. In her travels though, she has come to love each of the cities in their own way. Anymore I suppose, she tends to spend time at each of her (mage) guild halls or the University if visiting the IC. She travels so much that I suppose she would say she actually lives out of her mare's saddlebags. She really needs to find a roomie to share her small Bravil home since she is there so rarely.

I always end up in Bruma with my nord character --for some reason, I always end up as a Nord female... maybe because I'm a northern lady meself... Although Bruma feels like it's stuck in an internal slushy and grey spring that will not break open, I installed http://www.tesnexus.com/downloads/file.php?id=26625 mod (especially Snowy Leaves) which makes the area more winter like, as in the beginning of the season, when you feel Christmas is near. That's the best of the season, because after that, it gets boring and eternally long.
I like the feel of warmth you get when entering a tavern, sitting near a fire while all hell breaks loose outside. I also like the Nord accent, specifically the male big deep voice... hmmm. And it's nice to be recognized as one of their own. "Hello sister!" Plus, I got a fence near...

Skingrad.

Ok I′ll answer this question again and with the same answer, Bruma. Always felt like "my" hometown.

no bliss or crucible?

thread fail.

Hard choosing between The Imperial City and Skingrad. I went with Skingrad because I love Rosethorn Hall and it's Quest. My character also collects wines.

Chorrol.

It fit the image of "middle ages fantasy town" in my books. Plus, it's the first town I ever visited, and to me, at the beginning of the game, with those stunning graphics, the whole thing just blew me away. I was like; "OMGZ WE CANZ ACTUALLY TALK TO DA PEEPLEZ???!!!!11"

Good times.

Cheydinhal is beautiful. I can't understand why nobody voted for it.

I also like Chorrol though.

Skingrad.

Skingrad. It's got an awesome count, Rosethorn hall, all the shops you need and it's right at the foot of the Great Forest.

i like anvil. it is quiet, sunny, has a sandy beach...

Imperial city is the best. All the facilities of the mages guild with the best defence. A market area that has more shops than a town/village has normal buildings. The palace. The start of the game. The sewers. The arena.

Chorrol! Skingrads a close second though.

skingrad. best count, best house, best guard uniforms, and best town layout.