If you consider towns in recent Elder Scrolls or the Bethesda Fallout games as "hubs" (since you buy/steal a house and keep returning to it over and over again to sleep/level up/drop off loot/etc).
Seyda Neen (Morrowind): most people will never come back, but for those of us who love to hang out as long as possible (or come back later to break into the armory if you don't know the tutorial trick). The lighthouse, Arille's bar and shop, the smuggler's cave nearby, the soft calls of the silt strider: it's a great introduction to this world.
Skingrad (Oblivion): lots of dark corners make this a great thief city. The blend of Italian with gothic make it a beautiful place to run around in. And the house is the best house, arguably, in the vanilla game. Shops are just a few yards down the street.
Imperial City (Oblivion): not just because it's huge and has some fantastic quests, but the atmosphere is fantastic.
Vivec (morrowind): speaking of huge and atmospheric capital cities, Vivec city alone makes me wish we could get a remake with modern graphics.
Rivet City (Fallout 3): there's a reason many of the most popular housing mods add apartments to this area. Not only because it's the center of everything with lots of shops and some quests, but it's a fucking aircraft carrier.
? (Fallout 4): I've only played a bit but I already love that I get to create my own hub city. I can't fucking wait to finally jump into next gen and waste a day or two playing this. Once I get a PS4 I'm taking a week's vacation.
ALSO:
LA (Vampire Bloodlines): the music the music the music, the atmosphere, the characters, goddammit please god give me a sequel
Under City (WOW): my favorite area in the game. Spent hours HOURS just talking to friends and running around the circular city when we weren't questing or when preparing for a raid/dungeon (or when drama was so fun to read). The music is so chilling, yet head bobbing, so good. I would play a Forsaken videogame in a heartbeat.
Random Shelter (Project Zomboid) - I love the idea that your safe zone can become dangerous over time. Eventually your character can become bored, or zombies will hear you walking around and start attacking your barricades/windows or you'll start to run out of food and need to leave or someone will break in or...
McReady Farm (State of Decay) - speaking of which. There are a lot of great little houses in this game (or a church or a trucking company or a fairground) but this is the most atmospheric. With the little bear statue (get it? Bear...McReady...McReady from Thing...Bear McREARY from Walking Dead fame?) and the shady trees, it's also benefited by being in the center of the entire map. It's just a drive through the fields to get the city in the north or Marshall in the south or at least to hit the highway to reach anywhere else. Just make sure and turn the barn into an Outpost if you want to cut down on the constant Hordes heading up the road toward you (or coming from the fields near the orchard). I know it's a waste of an outpost, but motherfuck you don't want zombies spawning five feet from your fences.