Since ggplot2 is based on grid, subplots (more than one plot per device) can be created the grid way with these two helper functions:

subplot <- function(r, c) {
# select viewport from layout
#   used to do subplots
# Args:
#   r:  row
#   c:  column
# Returns:
#   viewport for plotting
 
    viewport(layout.pos.col=c, layout.pos.row=r)
}
 
vplayout <- function(r, c) {
# Set up grid layout for creating subplots
# Args:
#   r:  row
#   c:  column
# Returns:
#   viewport
  grid.newpage()
  pushViewport(viewport(layout=grid.layout(r, c)))
}

which can be used the following way (given two ggplot plot objects p1 and p2):

vplayout(2, 1)
plot(p1, vp = subplot(1,1))
plot(p2, vp = subplot(2,1))

Any of the more advanced grid viewport magic can be used as well. For example [inset plots)[http://learnr.wordpress.com/2009/05/08/ggplot2-plot-inside-a-plot/]. ggplot2 now also provides ways to add plot annotations itself.

###Update This method does not ensure that axes are aligned. A newer post describes how to do this.