I have a similar problem. Unlike the OP, I have the Adobe Creative Suite (or something like that) on my computer, and it includes Adobe Acrobat 8 Professional. I'm in college, so I'm always opening PDF files for lecture notes, etc. I was a long-time Firefox user, but recently decided to switch back over to Safari. Now when I open PDF files, it always opens them in a Safari window (i don't know if it has to do with Adobe Acrobat or not). When I click on a PDF file in Safari, I want it to open in Preview like Firefox did, and not the Safari window. It takes about 3 times longer to open a PDF in Safari as it does to open it in Preview.
I already did what another poster recommended: I went into HD > Library > Internet Plugins, and I deleted the PDF viewer plugin, and for some reason my pdfs continue to open in Safari. Secondly, my default program for opening PDFs saved to my computer is Preview.
Basically, I would like to be able to go to a course website, click on a PDF file, and have it download and open in Preview. Do you have any other ideas that might work? Or any ideas why the other solution may not have worked?