Do bitcoin exchanges based outside of the US who serve US customers have to register with FinCEN as MSBs? From what I understand, Bitstamp is not registered with FinCEN, whereas Mt.Gox is, does this mean Bitstamp is in danger of being shut down?
The short (slightly oversimplified) answer is that most consumer protection oriented laws (including Money Services Business and Money Transmitter laws) apply to the consumers themselves. So if you serve customers in the US, you must comply with the laws that protect those customers.

IANAL, YMMV, etc. Consult an attorney specializing in MSB/Money Transmitter laws for an more accurate application of the laws to your business model.