SEM: Bar chart of mean with +/- Standard Error of Mean (SEM) error bars.
CI: Individual data points are plotted for each sample. Confidence intervals (CI) for the estimation of the mean are plotted as a box with the mean marked as a horizontal line. These CI mark the confidence that the true mean falls within this range. By default, CI are estimated from the sample standard deviation (SD). Alternatively, the “true” CI based on the real SD of the population can be plotted.
BoxPlot: The boxes plot the interquartile range (IQR) of the data, such that half the data is within the box. The whiskers extend to the extreme points that are within 1.5IQR from the box. “Outliers” beyond this range are plotted as individual points. (See R
boxplot.stats help or this useful blog post for more on boxplots.