Not Shadowrun, but one of the characters I play in Mutants & Masterminds or Champions games took an old subway station in New York, one of the ones that had been shut down and sealed off when lines were redone, and made it into an awesome lair, complete with a security system that sprayed someone with liquid nitrogen if they didn't pass the palmprint scanner, retinal scanner, and voice analysis simultaneously within 30 seconds of typing in a 16 digit code. Was that paranoid? Hell yes. But he never once had to worry about someone kicking in his front door. Of course, he was also immune to cold damage, being an ice-type super, so the defense system didn't bother him.
Now, as far as Shadowrun, if we limit it to Seattle in particular (since that's the primary setting), there aren't any subway tunnels, since any that may have existed are now part of the Orc Underground (though if you're of the proper persuasion you could just live down there). However, there ARE almost certainly fallout shelters left over from the cold war, especially outside of the areas where they put up arcologies, say in the Tacoma area, or out in Puyallup or Redmond. Also out in the Barrens you have a whole bunch of abandoned facilities that could be picked up and secured into a base. If you want actual dirt to dig in, I'd suggest slipping just over the border into Salish lands, where there's more land to play with.
