Browser embedded PDFs should not be a built-in default option. To disable that, and have the PDFs open with the defaulted installed application, as they should, there are a few settings.
When I was using Firefox, this usually took care of that in terms of Adobe Acrobat:
Firefox > Tools > Options > Applications > Adobe Acrobat Document > Save to File
But other browsers, like Chrome, don’t provide as much customization options, so that calls for an Adobe Acrobat settings :
Acrobat > Edit > Preferences > Internet > Web Browser Options > Display PDF in browser
[UPDATE Jan 2012]
For Chrome, follow these instructions :
Just type (copy & paste), this into the address bar.
That will take you the page to disable plugins, as mentioned by JESSE ST.
Then disable “Chrome PDF Viewer”
This should take care of it in all browsers.
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