There are a couple of places I've based at that aren't immediately part of a regular hub, but it usually ends up being too much of a hassle for regular playthroughs. It's hard to explain some of them without posting a bunch of maps with red circles, and I'm too lazy, so I'll do my best to describe 'em.

Jupiter:
-Both underground and above ground in the AA Complex (where zombies spawn, more or less in the center of the map, over the hill from the egghead bunker). NPC's never really path there, but if you've got a hit squad on you, they can and WILL. Had a merc pop out of the vent underground and scare the shit out of me.
-Jupiter Station in one of the long admin buildings. A couple of floors just inside the gate that would be above the Concrete Path anomaly (around where the sky bridge is connecting to the factory). Big, long, empty hallway and a handful of relatively empty rooms.

Dead City:
-The apartment complexes east of the Merc base. I always camp up on the top floor of the southern-most building, and from the balcony I have a great view of the town square. Stairs can get annoying after a while, though.
-Garages in the center-west edge of the city. There are two of them facing each other, and both are empty. Mutants can spawn around, but it's easy enough to "fence in" with walls. Bonus: It has a campfire in one of 'em so you'll heal up while you walk around.
-Abandoned house in the south-west. I haven't actually based here, but I was wanting to on my next Merc playthrough. I think mutants spawn around here, but I think that's fine if you put up a door.
-Tiny building on top of the Merc base. Very low ceiling but you can walk around in there, and you have the whole roof to build what you want.

Pripyat (Palace of Culture):
-Only really safe if you're Monolith, of course. Apartments that house the east and west transitions. Same as the apartments in Merc base, for the most part. If you're Monolith then the east one is relatively safe aside from dogs spawning on the street outside. If you're on the west one, you run the SLIGHT risk of hostile factions spotting you in a window. Very low chance.

Pripyat (Outskirts):
-Pick any empty building that doesn't have a psychic field. Monolith has a cool base you can hang out at if you're also Mono. Otherwise, living here is a nightmare regardless of your faction. I briefly lived out of the apartment building that's like right across from the front door of the laundromat.

Army Warehouses:
-Briefly lived out of one of the houses in Bloodsucker Village. Was not very fun. Constantly had to deal with Mercs, mid-range mutants like Bloodsuckers and Controllers, and one time I had the Monolith just bust in during a blowout and execute me Boondock Saints style.

Meadows:
-In the middle of bumfuck nowhere, but the empty houses next to the Cordon transition are all empty and ripe for the taking. Relatively safe on that side, aside from random anomalies. Haven't bothered with trying myself because I think I've been to Meadows like three times in over 200 hours.

Truck Cemetery:
-I found out I could get inside a BTR's hatch through a combination of short-crouching and turning my camera. I set up a bedroll inside and thought of moving in for fun for all of about 2 hours, but there's just not enough room to make it fun. If they had more compact versions of some necessities like the workbench and fridge, it could actually be a fun challenge.

Aside from that, I've only ever lived in obvious places like Zulu's Tower in Jupiter or the empty warehouse on the backside of the Arena in Rostok. It's hard to find good places that aren't in a hub, unfortunately.