He is an authority on the legal aspects of emerging media and an advocate for Internet freedom, including increased online transparency[4][5] and accountability[6][7] as well as child safety.

[2][11][12] Palfrey served as finance director in Boston for the campaign of Lois Pines for the position of Massachusetts Attorney General.

[15] Berkman, under his leadership, also initiated efforts to combat malware, spyware and computer viruses with a program called StopBadware.

[24] While at Andover, he was elected as the chairperson of the Knight Foundation, a charitable organization which focuses on how information can improve democratic institutions.

[28] Palfrey is regarded as an authority about how people use technology, including how they relate to information and engage in politics in emerging digital media such as the Internet.

[29][30] According to Palfrey, digital natives (those born after 1980 and who grew up with the Internet) are more likely to "see relationships differently" as well as access information in new ways from previous generations.

[31] He is a supporter of information sharing while maintaining copyrights: We should figure out how to offer legitimate services that enable people to be accountable to one another online, using innovations like Creative Commons licenses, which make sharing legitimately much easier.In 2008, Palfrey served as the chair of the Internet Safety Technical Task Force, a year-long national effort to explore how children could "avoid unwanted contact and content" online.

[8][32][33][34] He believes digital literacy should be an important public issue in schools so that kids can "sort credible from non-credible information".

[36] He advocated flexibility in legal solutions for coping with cyberbullying, which happens when "kids treat one another awfully online",[35] and he recommended that laws not be too tied to specific technologies.

[42] Palfrey was a member of a pro bono legal team that helped defend street artist Shepard Fairey in a "fair use" case involving an Associated Press photograph of Barack Obama in his Hope poster.

[43] Palfrey urged Congress to write legislation to discourage prominent Internet firms such as Google, Yahoo, Microsoft, and Cisco Systems from bending to pressure by foreign governments to censor web information or forcing them to reveal the identities of dissidents,[4] as part of the Open Net Initiative.

[44][45] His work on how Internet usage can affect politics within democracies was cited as influential to the dissidents in Iran responsible for the Green Revolution.

These references resulted in his being named by the Iranian government, along with colleague Ethan Zuckerman, as a so-called "conspirator" in the trials that took place in Iran in 2009 and 2010.

[47] Palfrey emphasizes that while for-profit information sources like Google and Amazon are prevalent, they serve a different purpose—primarily profit rather than public access to knowledge.