Why would I use 2N3904 instead of 2N4401?
There may be good reasons for choosing the 2N3904 when working at lower current. The 2N4401's higher current capability comes at a cost - higher capacitance and much longer turn off time at low current.

Emitter-Base Capacitance:- 


2N3904 = 8pF
2N4401 = 30pF


Storage time:- 


2N3904 = 200ns @ 10mA
2N4401 = 225ns @ 150mA