I have been saving receipts, order confirmations, and so on from web commerce sites using the built-in Save PDF to Web Receipts Folder workflow in the "PDF" dropdown of the print dialog box. I was very surprised to learn (and you might be too) that this workflow silently overwrites existing files with the same name! Since it derives the file name from the web browser's window title (which in turn is derived from the tag of the web page), you can find yourself saving today's receipt from BogusSales.com, while clobbering your previous receipt from the same vendor (since the window likely has the same name on both occasions). You don't get a chance (1) to set the filename to something meaningful to you, or (2) to confirm that you want to overwrite.
But suppose you want to protect yourself from unintended file overwrites. You can always use Save as PDF instead, and enter your own filename and navigate to a storage location. That approach is safe, but lacks the one-click elegance of the Web Receipts solution. Also, the default Web Receipts folder may not be in the location you prefer. Can it be customized? Since Save PDF to Web Receipts Folder is simply an Automator workflow, you can modify it (or, to be safe, a copy of it) to better meet your needs.
Summary:
I opened the stock Web Receipts workflow in Automator. I was surprised to see it consists of a single step, New Folder, pointing to the Web Receipts folder. (If a folder with that name already exists, New Folder uses the existing folder; if files passed to New Folder, they are stored in the named folder.) So in front of that step, I added a Rename Finder Items action from the Finder library, and set the options to have it append the time of day to the filename of the file to be saved. That (almost assuredly) makes the filename unique, since the chance of twice saving a window with the same name at exactly the same hour, minute and second is remote.
I saved the copy in the PDF Services folder with a new name; it now appears automatically in the PDF drop-down in the Print dialog box. If you need more details on the how-to, read on...
Step-by-step:
Mac OS X Hints
http://hints.macworld.com/article.php?story=2007020700285547