How do you change file associations on an iPad? I would like to change .pdf files to use a different application when clicking on links in a browser.

How can I do this?
You can and you can't at the same time. Safari will load the PDF automatically and display it but it will offer a "Open In" button where you can send the PDF to another application if it is configured by the developer to accept PDFs (eg. iBooks, GoodReader, etc.) At present there is no way to direct it directly to another application unless that application will take a URL you could copy and paste.