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.
AND
fisking: n. [blogosphere; very common] A point-by-point refutation of a blog entry or (especially) news story. A really stylish fisking is witty, logical, sarcastic and ruthlessly factual; flaming or handwaving is considered poor form. Named after Robert Fisk, a British journalist who was a frequent (and deserving) early target of such treatment.
A really obnoxious term in my opinion.
John Thornton