There is a much better method I recently came across: "trellis plots". The package in R is called lattice.
This is clearly the way to quickly and neatly plot multifactorial data in lots of meaningful ways.
- Excellent Lecture on making trellis plots with lattice (pdf)
- some hype
- The online book on lattice
- code and figures from the book
- ** a table suggesting general forms for each type of plot (thanks Eldon)
install.packages("lattice", dependencies=TRUE) # I don't think there are any dependencies library("lattice")