By default, when writing a figure window to a PDF file, the figure's content is centered on an A4 or letter-sized page. This is not true for any other file format (EPS, TIFF, PNG, etc, where the bounding box of the resulting graphic, very sensibly, matches that of the figure window). This simple function sets the figure's PaperSize and PaperPosition properties so that the PDF file's bounding box matches that of the figure window.
<create a nice plot>
print -dpdf figure1.pdf
This function was created using Release 2011b, but should work for earlier releases also.