I have a polygon layer that I would like to print images or PDFs from in bulk as there are a large number of them. Rather than having to manually scroll and print each individual'site' in the print composer (QGIS 2.0 or ArcGIS 10) are there any tools that I could use or scripts etc?
For QGIS, have a look at the Atlas functionality in the Print Composer.
The idea is to have a "coverage layer" which contains all the "sites" that you want to zoom to and make a map of. Atlas has all kinds of functions which let you control the resulting maps, e.g. whether you always want the same scale or not.
Some new stuff which is not covered by the user guide yet:
For ArcGIS you probably want to take a look at Data Driven Pages:
"Data Driven Pages gives you the ability to generate a set of output pages by taking a single layout and iterating over a set of map extents. The extents are defined by the features in a layer and are sometimes called tiles, sections, or areas of interest (AOI). The layer that defines the extents is referred to as an index layer. Any feature layer may serve as the index layer. "