Some of the major journal publishers, such as Wiley and Nature, have added ReadCube as an option for viewing the full text of an article. Depending on which journal platform you’re on, you may see links for the article as a PDF and as an “Interactive PDF from ReadCube” or just one option. Here are some examples:

http://www.nature.com/nature/journal/v456/n7221/full/456450a.html

http://onlinelibrary.wiley.com/doi/10.1017/S1464793106007032/abstract
Although these “ReadCube PDFs” may be billed as PDFs, they have some flaws, as noted by researcher Ross Mounce, who finds that they are not clearly labeled on the article page by Wiley and that in some cases the images are messed up from the original PDF. In the case of Wiley’s interface, if you want the original PDF, you first have view the ReadCube PDF and then within the ReadCube interface look for the “Download PDF” option on the bottom; only then will you be able to the traditional PDF.
Interestingly, Mounce suggests that people who are concerned about the usability problems with how ReadCube is presented and functions, and with the DRM that is built into the technology, and with its possible privacy issues may actually want to block ReadCube PDFs from even appearing in their browsers and offers a range of browser plugins and security settings to do so.