I researched this awhile back, and thought it might be appropriate for this board.
'Fountain Pen', what does it mean?
The word fountain is borrowed from Latin [fontana (spring, fountain) from 'fons'] and can be traced back to the IE (Indo-European) *dhon-ti-, from the root *dhen- (to flow). Fountain, as used in 'fountain pen' is of the sense: "a reservoir or compartment for holding oil, ink, etc." (OED). However, the IE sense 'to flow' is certainly applicable to how fountain pens operate.
"Without any further Care [the lamps] received Oil as fast as they wasted it, (as in those which we call Fountain Inkhorns, or *Fountain Pens)- M. Henry (1710)
The word pen is borrowed from Latin [penna (feather)] and can be traced back to the IE 'pet (I)'- (rush, leap, fly, fall) and also gives us the Greek pteron (feather, wings). Considering the history of writing instruments, where the quills of feathers were split into two tines in order to form a writing instrument, it is not difficult to see the relationship between these cognates.
"With a Quill the one halfe cut away, or a Pen of steele (made thin for the purpose)" -Austen (1657)
For fellow word-watchers who are interested, references:
Onions, C.T (Ed.). The Oxford Dictionary of English Etymology. London: Oxford University Press, 1966.
Oxford English Dictionary CD (2nd Ed.). Oxford University Press, 1999
Shipley, Joseph T. The Origins of English Words. Baltimore: Johns Hopkins University Press, 1984