If you want to produce an animation, you better use specialized tools for it (like mplayer).
Use gnuplot to prepare all source images (first one with single row plotted, second - with two lines, etc), then use mplayer or convert (from imagemagic) to produce avi or animated GIF out of source files.
You can use the following shell snippet to produce partial copies of the input file, each with increasing number of lines.
file="your input file.dat"
lines=$(wc -l $file)
i=1
while [ $i -le $lines ] ; do
head -${i} ${file} > ${file%.dat}-${i}lines.dat
done
Given somefile.dat this will produce files "somefile-1lines.dat", "somefile-2lines.dat", etc. Then you can use:
for f in *lines.dat ; do
gnuplot ... $f
done
to plot them all in sequence.
If my assumption is wrong and all you really want is this pause, then you can try to set things up so that gnuplot will get data from stdin, and then use this scipt (name it paused-input.sh) to pipe input file with pauses after each line:
#!/bin/bash
while read l ; do
echo "$l"
sleep 1
done
Then invoke it like this:
(pause-input.sh | gnuplot ...) < somefile.dat