Best practice is to accept the impossibility of enforcing any protection mechanism, in my view. If this is not acceptable look at DRM e.g. LiveCycle Rights Management, but bear in mind that you will be locking out many people e.g. those with tablets, and confusing many more e.g. those with FireFox or Chrome.
To ensure they appear in any possible browser you would have to put your T&Cs on the page itself. Comments, layers and scripted popups don't work reliably on third-party software or in mobile apps.
If you apply password security with Acrobat you can turn off the ability to copy text and images in Acrobat and Adobe Reader. It's trivial to bypass that protection and most third-party applications don't even bother to enforce it in the first place; however by applying the restriction you are making it clear to your readers that you do not give them permission to extract content from the magazine. If they do it anyway, you can seek to enforce your terms and conditions in court. Most of the time a newspaper is fine with small-scale copying for personal use, and if a commercial agency tries to steal a story they know it will be found out.
If these PDFs are free to download then using DRM (the only way to truly protect your content as Test Screen Name says) will be far too expensive.
Okay I'll pack the T&Cs onto the website then. Thanks guys.