For the same rider without modifications and in order of decreasing return on investment:
wheels
tires
frame
gearing changes
clipless pedals
crank
saddle
handlebars
stem
seatpost
helium in the frame tubes
cables
handlebar tape
The first 3 can have a large effect on the bike's ride and speed. After that you're only gliding the lily.
By the way, putting helium in the tubes would be silly and would waste good helium. Changing cables and putting on new handlebar tape just to 'improve' the bike rank below that.