Client-side JavaScript will be the way to go. Although I don't know if there's code floating around to do this. Basically, you'd want to test if the PDF MIME type is available in the browser (good way to test all browsers that are not IE) or if the plugin can be accessed from JavaScript (good way to test IE). If you can do either, than the browser probably has Reader installed.
I don't think a lot of sites do this. They usually resort to putting an Acrobat Reader logo that points back to Adobe's website and then just provide links to the PDF. If they don't have Reader, then the PDF gets downloaded and they can then determine if they want to get Reader to view it. Keep in mind - installing reader will cause ALL browser windows to be closed.