Rich Kidd wrote in the ChemistryWorldBlog about Henry Rzepa to have published two papers in RSC journals where Jmol is part of the main paper, after having used Jmol in extra material in ACS journals before. The key here is that the Jmol is part of the official text... when you open the paper in a browser, you immediately get to see the Jmol live, 3D graphics! Well, so it is said in the blog.
However, when I checked the HTML of the first of the two papers (A computational investigation of the structure of polythiocyanogen, doi:10.1039/b810147g). The main HTML still links to a supplementary page. Progress, but not perfect either: