High-level analysis languages such as MatLab and idl have fairly good built-in plotting capabilities. If you are using one of these, you should most likely learn the associated plotting procedures. Traditional languages such as Fortran and C do not contain plotting facilities and thus a separate mechanism is required. The most common prodecure is to have the Fortran or C program write a data file, which can be read by a separate plotting package in order to make plots. In my opinion, gnuplot is by far the best plotting package to use. It can be installed free on Linux, mac, and Windows operating systems and contains extensive documentation.
You can try out gnuplot on the sample data file, using the following commands. Although there is extensive documentation available, you may be able to find your way well enough with the gnuplot quick reference card