In recent times, there have been two ways to rank think tanks:
1) By nominations from people knowledgeable about think tanks: The University of Pennsylvania Think Tanks and Civil Societies Program's 2011 Global Go To Think Tank Index Rankings; this is updated annually; Dr. James McGann, author of the report, wrote an article about the 2011 report in the Diplomatic Courier.
2) By citations in the media: Fairness and Accuracy In Reporting, or FAIR; the last survey was conducted in 2008.
Forbes' Jeff Bercovici speculates that the FAIR think tank citation survey is no longer around because citations for think tanks have been in decline.
The Center for Economic Policy Research (CEPR) has this interesting memo from September 2009 on the cost effectiveness of the most widely cited think tanks.
As David Roodman of Center for Global Development (CGD) has pointed out, there is no perfect ranking for think tanks.
The site On Think Tanks has points out several critiques of the Global Go To Think Tank Index Rankings and has links to other critiques.
How else can we rank think tanks? By Google/Yahoo/Bing hits? By TV appearances of scholars? By think tank affiliates going into the current Administration? By number of times scholars testify before Congress? By number of events held? By budget?