[jtkung]

This is a hard one, as there are so many out there. But there a few that require mentioning as they have made a name for themselves for the quality of their work and customer service.
These guys are in the same class. Still not mass manufactured, but not made by one person either. High quality with reasonable numbers made per year:

• Suhr
  
• Tom Anderson
  
• Grosh
  
• Lentz
  
• Tyler
  

More exclusive, fewer numbers made:

• Parker
  
• Artinger
  
• Myka
  
• D'Pergo
  
• Thorn
  
• Stevenson
  
• Koll
  
• Sankey
  
• Ritter
  

There are many more in this exclusive category ...

Mainstream

• PRS Private Stock. As exclusive as the others above but not made by a single builder. Known more for exotic woods and extra bling
  

No mention of custom shops from the big boys (Gibson, Fender, Ibanez). These are all made by multiple people on a pseudo-assembly line. Not by a single luthier or master. You are better off going to a specific luthier.