I've been working on a demonstration web site of a meningitis case reporting system in Africa. The current demo uses OpenLayers to show a map of the spatial distribution of cases, and a couple of PNG plots generated from R to show the cases in time for a particular area. One plot showed the cases for the past year, and one was a plot of the previous four weeks with our prediction of the next four weeks cases (plus 95% confidence interval).
Flot - although jqPlot looks pretty capable too.
Flot lets you plot lines, points and bars, and you can make filled areas by constructing a data series that goes along the top and back along the bottom, completing a polygon. You can shade and style the points and lines, and you get a legend. If your X-axis is time, you can feed it milliseconds and get dates. Here's what I've got to start with:
Flot also allows zooming in on plots. See that earlier peak around July? We can select that area:
plot = $.plot(plotDiv, d, options );
If anyone wants some more code, or the full example, then just ask!