At New APPS, although we encourage the use of real names,* we also allow anonymous and pseudonymous commenters. Most of the time there are no problems, but sometimes anonymity or pseudonymity allows for, (or even encourages?) trolling** or just plain jerkitude. (It's not that people can't be trolls or jerks with their own name; it's just been my experience that most trolls -- if not jerks -- take advantage of the cover of anonymity or pseudonymity.)
But even beyond the trollishness or jerkitude there's something annoying about anonymous or pseudonymous trolls / jerks: it's insulting to the named interlocutor, as if that person would try to exact some meatspace revenge on someone for a blog spat! Even if someone could (but how? Write a letter to their department chair or dissertation advisor?), that's a terribly insulting thing to say to someone that they are so petty that they would.
* when I entered the US university political economy of teaching, which I did as soon as I became a TA (for me, immediately post-BA), there was no blogosphere. (I didn't wear an onion on my belt, though.) So I never had to face the question of using my real name when commenting on blogs. Now this has probably been discussed at length among current graduate students, so forgive me if it's obvious or clueless or insensitive, but it's at least possible that commenting with your real name can help your brand name: write smart, serious / witty comments and you may, albeit very, very marginally, help your job prospects. But maybe I'm not sufficiently attuned to the relevant risk-reward calculations?
** The problem with most trolls is their mediocrity. A good troll is an artist, and I would be thrilled beyond words were the Prince of Trolls, Floyd Alvis Cooper, or the Dark Lord Himself, Venus_Montgomery, to visit New APPS.