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.
Type help iteration at the gnuplot command line for more info.
Also be sure to see @DarioP’s answer about the do for syntax; that gives you something closer to a traditional for loop.