I often click PDF links in Safari, and the PDF will open in that Safari window rather than downloading. This is ok with me. I don't like a bunch of files cluttering my ~/Downloads folder.
But when I do want to download one of these PDFs, there isn't an easy way to do it. There is no "Save As..." in the right click menu, and the HUD buttons at the bottom of the viewer are hard to reliably bring up.
Enter this Automator workflow, which I trigger with LaunchBar. It will download the file (PDF or otherwise) in the frontmost Safari window into the frontmost Finder window's folder, or to the Desktop if no Finder windows are open. Download it here.