Calyx got the subpoena in connection with a Justice Department investigation into the posting of an RNC delegate list -- it was posted to Indymedia websites as well as elsewhere on the Web. The investigation itself seemed intended to chill First Amendment-protected expression, but because they had nothing to disclose, ISP Calyx and Indymedia were not chilled. Calyx was able to turn over all the information it had, the email addresses of four administrators, and avoid being called to testify before the grand jury. The Indymedia administrators, in turn, knew their machines could not provide any further information for the investigation.
Indymedia's FAQ states that "Indymedia sites are spread across many servers and we do not log IP addresses as a way of protecting the privacy of our visitors." As Indymedia admin Brian Szymanski told Wired News, Indymedia allows for anonymous and pseudonymous posting as well as posting associated with registered email addresses, which the site does record. "Anonymity has always been essential to what Indymedia is trying to do because we want to empower all citizens to make their own news and write about what they find to be important," said Szymanski. "We have whistleblowers or victims of government harassment and sometimes they need to be protected by anonymity."
Indymedia had adopted its anti-logging policy several years ago, after being targeted by an FBI investigation of anti-FTAA protests in Seattle. For those concerned about free speech who haven't yet adopted similar policies, EFF has prepared a set of legal and technical recommendations, best practices for online service providers, for limiting the logs you keep. For more detail, see the EFF whitepaper [PDF].