My personal favorite is a shack at the top of a large cliff...its got an excellent view, and some amazing supplies inside for workbenches
Ahh the sniper shack..good times good times.. :gun:
My favorites are usually any number of the powerstations, particuarly the MDPL Mass Relay Station (when all the raiders are enslaved and gone)
I also always thought the clifftop shacks would be a good base for an evil character (if the supermutants were gone) and if the wkml broadcast station had a bed I would have mostly used that as my house instead of just as a storage shed.