Acrobat Pro (6 & 7) has a built-in feature that lets you quickly identify the differences between any two PDFs. This can be a godsend when confirming that all needed copy edits were made in complex documents or confirming corrections in long documents (book publishers love this feature).
Open two PDFs you want to check for differences, and choose Document > Compare in Acrobat Pro (Acrobat Standard doesn’t have this feature).
In the Compare Document dialog box, select the two documents you want to compare. Then select whether you wish to compare the documents visually or by the text changes.
Page-by-Page Visual Differences will highlight differences in image, color, and text. This is best for identifying changes in the layout or placed graphics.
Textual Differences highlight differences on the copy alone and gives you more details (e.g., which words were inserted/deleted).
Source: Anne-Marie Concepcion in the wonderful DesignGeek newsletter. While we are avid readers of DesignGeek, it was the January 2006 issue of Design Tools Monthly that first turned us on to this Acrobat Pro technique.