Nicole Perlroth, Jeff Larson, and Scott Shane of the New York Times report:
The agency has circumvented or cracked much of the encryption, or digital scrambling, that guards global commerce and banking systems, protects sensitive data like trade secrets and medical records, and automatically secures the e-mails, Web searches, Internet chats and phone calls of Americans and others around the world, the documents show. […]
The agency treats its recent successes in deciphering protected information as among its most closely guarded secrets, restricted to those cleared for a highly classified program code-named Bullrun, according to the documents, provided by Edward J. Snowden, the former N.S.A. contractor.
The Times isn’t reporting specifically which algorithms have been broken or are susceptible—to do so would immediately drive people away from those algorithms. They only mention SSL, VPNs, and the encryption used on 4G cellular networks.
Bruce Schneier has written a manifesto urging engineers to rebuild the internet to make it harder for governments to spy. He’s also written about what you can do to stay safe in the face of pervasive government spying.