"The New York Times and ProPublica said they were asked not to publish their findings by intelligence officials who argued that their foreign targets might switch to newer forms of encryption or communications if the NSA tactics were revealed. 'Some specific facts' were removed, the New York Times said. The articles do not say which mainstream encryption systems have been effectively broken."
The Times includes "Complete enabling for [XXXXXXX] encryption chips used in Virtual Private Network and Web encryption devices." http://www.nytimes.com/interactive/2013/09/05/us/documents-r...
(compare to http://www.theguardian.com/world/interactive/2013/sep/05/sig... )