R provides several frameworks for composing figures. Base graphics is the simplest, grid is more advanced, and the lattice/ggplot packages provide convenient abstractions of the grid graphics system. Multi-element figures can be readily created in base graphics using either par() or layout(), with analogous functions available in grid. Mixing the two systems is a little more complicated, somewhat fragile, but entirely possible.
I recently needed to combine base+grid graphics on a single page; two sets of base graphics on the left, and the output from xyplot() (grid) on the right. Following some tips from Paul Murrell posted on r-help, the solution was fairly simple. A truncated example of the processes is listed below, corresponding to the attached figure. While the result was “good enough” for a quick summary, there are clearly some improvements that would make figure more useful.