I think grouped bars are preferable to stacked bars in most situations because they retain information about the sizes of the groups and stay readable even when you have multiple nominal categories. For me, the segments of stacked bars get difficult to compare beyond two categories - and even with just two categories, they can be quite deceptive if your groups are of very different sizes. I'd prefer a frequency table over a stacked bar plot any day.
You should also consider a stacked series of bar plots, with each group in a separate plot and each plot stacked on top of the last (there's an example on this page, referred to as "layered histograms", which I find confusing). This is probably what I use most often. The lattice and ggplot2 packages in R both support this kind of plotting.
Historical note: histograms != bar plots