The term refers to Robert Fisk, a journalist who wrote some rather foolish anti-war stuff, and who in particular wrote a story in which he (1) recounted how he was beaten by some anti-American Afghan refugees, and (2) thought they were morally right for doing so. Hence many pro-war blogs -- most famously, InstaPundit
-- often use the term "Fisking" figuratively to mean a thorough and forceful verbal beating of an anti-war, possibly anti-American, commentator who has richly earned this figurative beating through his words. Good Fisking tends to be (or at least aim to be) quite logical, and often quotes the other article in detail, interspersing criticisms with the original article's text.
Responding to an earlier declaration against the war by a group of German intellectuals, a group of American academics and intellectuals has written a response. It's basically a heavyweight group-Fisking.