EFF is not "endorsing" Bitcoin in the sense usually meant; they're saying they'll accept donations that way.
The Activism Director of EFF wrote a substantial blog post on Bitcoin, calling it "a step toward censorship-resistant digital currency". Earlier, they had another post listing Bitcoin as a project that "digital activists" should contribute to.
ETA: Even without these explicit endorsements, it seems obvious to me that a prominent activism/lobbying/legal organization does not just do something like accept donations in Bitcoin without considering what kind of signal that sends.
Now you can donate to Singularity Institute using Bitcoin.
Currently Bitcoin mining appears to be profitable as only bubble economics can be. Already some Less Wrong users have purchased GPUs and started mining Bitcoin. Please consider sending some Bitcoins to SI at address 1HUrNJfVFwQkbuMXwiPxSQcpyr3ktn1wc9
2014 Edit: Please donate Bitcoin by using the Bitpay link on MIRI's donate page. Thanks!