I really liked Lattice for generating graphs in R until I saw what ggplot2 can do …
One of the big differences between the two is the theory on which ggplot2 is based upon. There are clear modular building blocks that can be applied in a consistent manner on any graph generated. Both packages are extremely versatile but at the end of the day I think ggplot2 provides a clearer structure and hence more flexibility …
Hadley Wickham (the author of ggplot2) has a book out on ggplot2 at Springer. Some sample chapters can be downloaded from his webpage.
The learningR people have a long series of posts where they provide ggplot2 code for nearly all the graphs in the Lattice book … worth taking a look at!
Here is an in depth