All my recent plots are built using ggplot2 package. I don’t know if my dear readers have noticed the difference, but from my point of view, ggplot2 allows to create nice looking and aesthetics plots. I was using this package before, but the real boost came after reading this book: ggplot2: Elegant Graphics for Data Analysis (Use R).
You can find a decent ggplot2 manual on internet, but the book is special, because it explains the grammar and the syntax. Then you know that, it is much easer to tackle various problem, for example – how to set transparency of the point, fill the color of the density plot and etc. Check my recent post as an example.