Jailing of political dissenters? Oh yeah, you bet! Hell, he even deported one notable Copperhead to the Confederacy (Rep. Vallandigham...more on that below)! As far as torture is concerned, though: no. At least not in the formal sense. One could make a case for the fact that being held without trial or due process in a dank cell with no real rights or privileges is a kind of torture. But if you're referring to proper feet-to-the-fire stuff, or direct orders to make a political opponent suffer, then no.

Just a few examples of jailing: (1) In 1861, John Merryman, a state legislator from Maryland, tried to block the passage of Union troops through Baltimore. Lincoln threw his sorry butt in jail, and when Merryman's lawyer demanded a writ of habeas corpus so a court could decide on charges, Lincoln famously suspended that very writ. (2) In 1864, Lincoln issued an Executive Order authorizing the immediate arrest of any newspaper editor or proprietor that printed falsehoods or gave aid to the enemy. You can actually read the official order here: http://www.presidency.ucsb.edu/ws/?pid=70018. (3) In 1863, Lincoln ordered the arrest and eventual deportation of Clement Vallandigham, a House Rep. from Ohio. Vallandigham was a vocal Copperhead (an anti-war northerner), and was tried before a military court because of a speech he made that Lincoln (and many others) deemed critical of the Union.

These are just a few examples. Some quick Google research on the subject will lead you to a lot of information on Lincoln's aggressive use of wartime powers to clamp down on dissent in the North. Most of the modern historiography agree that while Lincoln probably over-stepped his bounds a bit in this regard from a Constitutional standpoint, his actions are largely justified within the context of the time, and situation(s). A full-blown Civil War is not a time to tip-toe through Constitutional ethics, and Lincoln's actions throughout the war demonstrate a consistent pattern of a President doing whatever he could to keep the country together. The very fact that this was not done in a malicious way, certainly not using torture as some might suggest, paints a picture of a no-nonsense yet largely good-intentioned man behind the myth.

[Sources: Harold Holzer, 'Lincoln and the Power of the Press'; Bruce Catton, 'Mr. Lincoln's Army'; Doris Kearns Goodwin, 'Team of Rivals']