Is Jack Bauer an antihero?

Depends on who you ask, really.

Wikipedia describes an antihero as following:

The antihero or antiheroine is a leading character in a film, book or play who lacks the traditional heroic qualities such as idealism, courage, nobility, fortitude, moral goodness, and altruism.

It is quite obvious that Jack Bauer does not lack idealism, courage, fortitude or altruism. However he commonly sacrifices moral values for the "greater good" by torturing people to stop the bad guys from killing innocents.

So he certainly is not your classic Ideal Hero who fights with honor, but, as you mentioned, he has many qualities that don't fit with the classic antihero either. He does not abide by the law or by moral standards, but he justifies it by the honorable goal he wants to reach.

Unfortunately with this he is not alone. Many villains pretty much live by the same standard: Do evil to reach good. So it can be argued that Jack Bauer is in fact a Well Intentioned Extremist and the only thing that prevents him from being a villain is that we are being told the story from his point of view.

The fact that he even has a torture trope named after him, the Jack Bauer Interrogation Technique, does not help his reputation either. And so TvTropes seems to clearly put him in the antihero category:

For all intents and purposes, this is Cold-Blooded Torture. [..] Of course, anyone who does this is usually at least an Anti-Hero to begin with.

In summary: It's not really a clear-cut case, but I would personally characterize Jack Bauer as an antihero. His good intentions and the fact that he is fighting against terrorists save him from being a villain, but for me his moral standards are not high enough to call him a hero in the classical sense.

Not a direct answer, but found it worth mentioning.

Monika Bokiniec has written a rather nice paper "“Who can find a virtuous CTU agent?” – Jack Bauer as Modern Hero, Antihero and Tragic Villain" – where various aspects of the character is analyzed. To quote from page 13:

             Another way of finding the middle ground between hero and villain is the idea of antihero. There is no clear definition or agreed upon theoretical description of an antihero, as it is the case with, e.g. the category of tragic hero. Therefore, following this line of interpretation is risky and debatable, but nevertheless, let us try to see how Jack fits here. […]

Though I do not agree with everything in the 19 pages long paper it touches upon and give the topic a good talk. It is absolutely worth the read.

Note that it contains some spoilers for season one, six and seven in particular and also some of the outline of season eight.

To make this notice/answer more self-serving I quote the rest of the mentioned section. Note that it continues in the paper:

Antihero has human flaws, he is gritty and disillusioned, as Jack sometimes is, he rejects traditional values and is more selfish than ready for scarifies, he usually has good intentions but they are unrecognized by his society and, in consequence, he is often misunderstood and rejected by it. Sometimes he uses immoral means for moral ends, but other times he is described as greed, violent and seeking selfish revenge. In a way it all comes down to creating and following his or her own moral code, just as Dexter does (who probably fits the antihero model better than any other contemporary TV character). Antiheros are at times characterized by inner conflict between villainous and heroic qualities, which would perhaps apply to some phases of Jack’s development. Still, I would remain a little reluctant to use the antihero label because when we place ourselves in the moral middle ground between the hero and villain we risk finding ourselves in the moral no man’s land.
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