brew install gnuplot
plot '< sort -n file3' using 1:($2-$3) with lines
There sure is (in gnuplot 4.4+):
plot for [i=1:1000] 'data'.i.'.txt' using 1:2 title 'Flow '.i
The variable i can be interpreted as a variable or a string, so you could do something like
plot for [i=1:1000] 'data'.i.'.txt' using 1:($2+i) title 'Flow '.i
if you want to have lines offset from each other.