Gnuplot
I use Gnuplot for any kind of plotting. It is a cross-platform command line tool for plotting data in 2D and 3D diagrams. It is both fast (for quick visualization) and detailed (for professional reports).
An example of how to plot the (x,y) data you describe would be:
plot "<filename>" using 1:2 with lines
which could be abbreviated as plot "<filename>" u 1:2 w l
. For more detailed plots and styles, you'll need to write script files, which are intuitive and easy to learn. The documentation is pretty detailed, and you could directly output your plots in many different formats, including Cairo PNG, TikZ, PostScript, and others.
Summary: Gnuplot is
- Cross-platform: runs on Linux and Windows
- Easy to learn and use: Simple commands that are mostly in natural language
- Plots 2D data from text files