Seeing as how nearly none of those that truly meant anything to me are still independently owned by the same people that started them, and aside from some of the already mentioned builders and companies that, regardless, maintain at least a semblance of their original identity, aesthetic, sense of humor, adventure and innovation, I'm going to go with the aforementioned Steve Potts and this week's big new/old obsession of mine: Curtlo.
If I was going to buy a modern, non-custom anything, from an older company that's still around, I'd probably go with a Moots or Ritchey. Just because some of their bikes at least feel connected in some way to some of their past designs.