People tend to either love them or hate them, but without question the most powerful "indy journalism" institution in the world is WikiLeaks. It is an online platform for whistleblowers and people with secret information, allowing them to pass on documents proving deep government or industry corruption.
WikiLeaks was in the news recently because its founder and editor-in-chief, Julian Assange, was driven into exile over charges of sexual assault against him right after the largely-anonymous group released Iraq War-related video and then US government diplomatic cables documents, starting in 2010. All but one of the sex-assault-related charges against Assange were dropped in August.
Meanwhile, WikiLeaks continues to crank out data and in May announced a partnership with the grassroots group Transparency Toolkit’s ICWatch project, in part because the group's members received so many death threats after opening up a searchable database of LinkedIn pages of people who work in the weapons industries. Here is the announcement from a few weeks ago. Fascinating website too.