Yes, it's the ONLY first century reference to Jesus outside devotional literature, that is agreed to be genuine by the bulk of scholars. The other Josephan reference (the "Testimonium Flavianum", Ant. 18.3.3) is very much more controversial, and there is no reference to Jesus at all by any other first century author.
There was a passage of Josephus mentioned by all the early Church fathers Hegesippus, Clement, Origen (I think) about how the death of James led to the destruction of Jerusalem.
Eisenman says that after Irenaeus, this passage is no longer found in Josephus, because it offended people who thought it should be about Jesus.
I think he is talking about this passage:
http://www.biblestudytools.com/history/flavius-josephus/war-of-the-jews/book-4/chapter-5.html
...
I should not mistake if I said that the death of Ananus was the beginning of the destruction of the city, and that from this very day may be dated the overthrow of her wall, and the ruin of her affairs, whereon they saw their high priest, and the procurer of their preservation, slain in the midst of their city. He was on other accounts also a venerable, and a very just man; and besides the grandeur of that nobility, and dignity, and honor of which he was possessed, he had been a lover of a kind of parity, even with regard to the meanest of the people; he was a prodigious lover of liberty, and an admirer of a democracy in government; and did ever prefer the public welfare before his own advantage, and preferred peace above all things; for he was thoroughly sensible that the Romans were not to be conquered. He also foresaw that of necessity a war would follow, and that unless the Jews made up matters with them very dexterously, they would be destroyed; to say all in a word, if Ananus had survived, they had certainly compounded matters; for he was a shrewd man in speaking and persuading the people, and had already gotten the mastery of those that opposed his designs, or were for the war.
And the Jews had then put abundance of delays in the way of the Romans, if they had had such a general as he was. Jesus was also joined with him; and although he was inferior to him upon the comparison, he was superior to the rest; and I cannot but think that it was because God had doomed this city to destruction, as a polluted city, and was resolved to purge his sanctuary by fire, that he cut off these their great defenders and well-wishers, while those that a little before had worn the sacred garments, and had presided over the public worship; and had been esteemed venerable by those that dwelt on the whole habitable earth when they came into our city, were cast out naked, and seen to be the food of dogs and wild beasts. And I cannot but imagine that virtue itself groaned at these men's case, and lamented that she was here so terribly conquered by wickedness. And this at last was the end of Ananus and Jesus...
So, if the references here were originally to James instead of Ananus (whose description elsewhere in Josephus is very different to this one), then might the Jesus mentioned here be our "Jesus"?
Just a thought...