Depends on the customer - if it is a government agency and SHA2 is mandated for their own passwords (per NIST standards), we comply (with a huge number of iterations based on CPU/GPU target specs). Additionally, we automatically increase iterations over time as CPU/GPU targets change - something a customer never needs to worry about (which is nice). Otherwise BCrypt or SCrypt is used for most customers.

It seems like some of the finer points of your concerns aren't being covered in this thread (e.g. # of iterations, if sufficiently high, will probably address your GPU concerns). Unfortunately for me, I can't read Hacker News all day and must move on, but if you'd like, definitely give us a call at Stormpath and we'd be quite happy to geek out and talk through the all of the details. (And I apologize if any of this came across as negative - no coffee today I guess).