I'm kind of an oddball, i tend to use things that are not that common because they make my character feel special depending on the personality he's portraying.
For my Legion playthrough i use the Bradley's shack cause it has that heavy militant feel and screams "WAR NUT".
http://fallout.wikia.com/wiki/Bradley's_shack
For my scavenger playthrough i use the Cliffside camp, gives my rugged, old, long bearded survivalist a relatively safe place to crash and store his cheap booze.
http://fallout.wikia.com/wiki/Cliffside_prospector_camp
Abandoned BoS bunker is a perfect home for my disillusioned roving BoS Paladin.
http://fallout.wikia.com/wiki/Abandoned_Brotherhood_of_Steel_bunker
Prospector's den is what my greedy scavenger calls home. Kill the Jackals standing in front of it and enter. Initially, the Prospector's Den will be inhabited by Jackal gang members, who have raided the den and killed the prospectors inside.
BUT, if you clear out the location off murderous cosplayers, a new group of prospectors, including two New California Republic prospectors, will inhabit the den for the rest of the game. Along with the two prospectors, a merchant will also inhabit the area, standing near the exterior of the shack, making it an awesome place to sell your stuff and live at the same time.
http://fallout.wikia.com/wiki/The_Prospector's_Den
But a single place for living i simply freakin adore is this little beauty called Hell's Motel. It's accessed via couple of bridges swinging above radioactive hot pools. Clear out the ghouls in front of it and the crazed Mr. Handy inside and it's all yours. The interior is big (lab, a kitchen on the first floor, sleeping quarters on the second), unique and nicely furnished. Um.........well, some bleach will take care of the blood stain
Despite the widespread radiation outside near the irradiated lake, Hell's Motel is radiation-free inside. And yes, i have a hard-on on this particular location.
http://fallout.wikia.com/wiki/Hell's_motel#Hell.27s_motel
Another awesome place is the Scavenger platform in the middle of Lake Mead. Just clear the lakelurks and drag their bodies (and pieces of it) into the water so they don't repawn after a few days.
Also, check out the Brewer's beer bootlegging, the basement is awesome.
http://fallout.wikia.com/wiki/Brewer's_beer_bootlegging
Of course, you can always use Novac or Lucky 38