Boxplots are a good way to get some insight in your data, and while R provides a fine ‘boxplot’ function, it doesn’t label the outliers in the graph. However, with a little code you can add labels yourself:
The numbers plotted next to the outliers indicate the row number of your original dataframe. Admitted, it could look nicer, but it’s enough to find your outliers back in your data.

It’s done by this code:
#create boxplot boxdata <- with(data,boxplot(dependent ~ condition1 * condition2, range=4)) #for each outlier in boxdata for(i in 1:length(boxdata$group)){     #add text to the boxplot     text(boxdata$group[i], boxdata$out[i], which(data$dependent==boxdata$out[i]),pos=4) }

You can download the code here.