I am starting to use ggplot2. I have some small n (about 30 or so) granular data with lots of overlap. Neither jitter nor alpha (transparency) are suitable. Instead a stripchart
You want to use geom_dotplot from ggplot2
you will probably want to use:
ggplot(insert your arguments here) + geom_dotplot(binaxis = "y", stackdir = "center")
Hope this helps. The results will look really clean which is what I think you want.