Jacob Emden was regarded as one of the outstanding scholars of his generation. He disapproved of the pilpul method of Talmud study. He was interested in secular works (he knew German, Dutch, and Latin), but he was a fiery opponent of the Shabbateans. Except for a brief period of time when he served as the rabbi of Emden, he was never an elected Jewish authority. This gave him the time to write sharp, critical pamphlets about his society.
His main historical importance lies in his campaigns against the Shabbateans. He relentlessly examined and investigated every suspicious phenomenon pertaining to the sect. He called upon the contemporary rabbis to publish excommunications and mercilessly attacked anyone suspected of supporting or showing sympathy to the Shabbateans.
The Shabbateans were accustomed to introduce hints of their secret doctrine into their literary works, particularly in the field of Kabbalah. Consequently, Emden became an expert in uncovering such allusions and hidden meanings, and developed an extraordinarily sharp critical faculty by which he could recognize any suggestion of the Shabbatean heresy. Many books in which no one saw anything to which objection could be taken, were condemned by him as heretical. Though at times he was at fault and suspected the innocent without cause, his judgment in general was sound.
His most famous controversy was with Jonathan Eibeschutz, rabbi of the "Three Communities:" Altona, Hamburg, Wandsbek. It was a position for which Emden had applied.
In 1751, Emden found some amulets which Eibeschutz had written. He published an article interpreting them as Shabbatean. All hell broke loose. The ensuing conflict divided German Jewry into two camps and undermined the prestige of rabbinical institutions. Although Emden eventually lost the battle, he continued to fight.
Emden went after the Zohar, the bastion of the Shabbateans. The Zohar was regarded by many as second only to the Bible in sanctity. Emden had questioned its antiquity, and consequently its sanctity, which provoked opposition.
Next, Emden questioned the Guide For the Perplexed, which he found to contain heretical tendencies; he did not believe that Maimonides was its author.
Although uncompromising in his Jewish lifestyle positions, Emden (like Eibeschutz) liked Moses Mendelssohn.
Sources: Gates of Jewish Heritage