GNU plot is very helpful for plotting data and quite powerful too. After some searching I found the book GNU plot in action.
I fount this website very useful for surface plots :
http://lowrank.net/gnuplot/plot3d2-e.html
This is another useful reference :
http://www.phyast.pitt.edu/~zov1/gnuplot/html/intro.html
This always helps : http://www.gnuplot.info/.
Hint: I think its a good idea to use awk to combine different columns. etc