I have the Adobe PDF Reader Plug-in which allows you to see .pdf files in your browser online rather than download them to disk.

The only problem is, I don't know how to turn that function off when I want to download instead of view online.

I am using Acrobat Reader 5.0 with IE 5.0. Can someone tell me how to disable the viewer?

just right click the link and hit "Save Target As"

Now going the other way, how do I enable it on OS X with IE 5.2?

Try reinstalling the program.