One of the most useful graphs you can produce in R using the plot(...) function is one with nothing in it. Using the type="n" option, you get a blank canvas to which you can add points, lines, text, shaded regions and build up something that's really very useful. Other packages such as lattice and ggplot2 produce really nice graphics, but when it comes to annotating these graphs and tailoring them to your needs you have to delve into more complex options and programming (panel functions) and this has quite a steep learning curve. Keeping it simple with the plot(...) function and using lines(...), points(...), text(...), polygon(...) etc. allows you to build quite sophisticated graphs without too much hassle.