To answer the original question, it depends on the situation. In a debate, ad hominems are virtually always logical fallacies. In a courtroom, however, they are perfectly acceptable.
I think the reason for that is that the nature of the argument being advanced in a courtroom is typically very different to the type of argument found here. Consider these two hypothetical examples:
1. (JREF)
Poster 1: It's clear to me that Steven Jones's microsphere analysis shows elements that could only have possibly been present due to thermate.
Poster 2: Steven Jones is a well known kook, so you're wrong.
2. (Courtroom)
Witness: I clearly saw the man who robbed my shop, and despite the balaclava covering the bottom half of his face I'm certain it was the defendant.
Counsel: The defendant is Jewish, and you're the editor of the newsletter of a local anti-semitic organisation, so your testimony should be disregarded.
The first example is clearly an ad hominem fallacy, because the character of the person advancing the argument is irrelevant to the content of the argument. In the second example, the witness is in effect appealing to his own authority, and the attack on his motives is therefore crucial to the evaluation of his honesty. Therefore, the ad hominem in this case isn't a fallacy.
We have a regular poster on the CT forum who claims that his expertise in marine architecture makes him an authority on the WTC collapses. Addressing that assertion isn't, therefore, an ad hominem fallacy, but a legitimate part of evaluating his claims, even though it's an approach that addresses the arguer rather than the argument. As far as I can see, though, that's about the only circumstance where ad hominem isn't fallacious.
Dave