American "2N" numbers were intended to be generic, i.e. independent of manufacturer, with parameters registered at JEDEC. (It looks like the acronym JEDEC is now a word, their website no longer lists the meaning of the abbreviation.) European and Japanese devices have different prefixes.
The meaning of the prefix is:
1N: diode
2N: triode (e.g., bipolar PNP, NPN, JFET, MOS triode)
3N: more electrodes (e.g., dual-gate MOSFET)
4N: even more electrodes (e.g., photocoupler)
"PN", "MMBT", and similar prefixes were originally manufacturer-specific, but were often copied by competitors.
The "3904" in 2N3904 is merely a number assigned when the device was registered, in order of registration.