There are several regulatory organisations involved in air transportation. International Air Transport Association and International Civil Aviation Organization are a couple of the most usual ones, and they have developed codes for such things as airlines, airports, etc. "B6" is the IATA code assigned JetBlue, "JBU" is the ICAO code. THe non-standardisation is the same for airports: B6 hubs out of JFK, according to IATA, but according to ICAO, they fly out of KJFK.

"IATA Airline Designator Information

Two digit Airline Designator - The designator is used to identify an airline for all commercial purposes. the two character airline designator is assigned by IATA in accordance with the provisions of Resolution 762. The two character airline designator listed are for use in reservations, timetables, tickets, tariffs, air waybills, schedules publications and in airline interline telecommunications, as well as for the airline industry applications. IATA assigns three types of two character airline designators. Unique, numeric/alpha and controlled duplicate." (Airline Codes Web Site)

More, not to mention lots of codes, at the Airline Codes Web Site.