The Compassionate Side of the Medieval Inquisition

Drawing: Two priests ask a heretic to repent as torture is administered.
From Wikipedia:
Investigation
When a papal inquisition arrived at a town it had a set of procedures and rules to identify likely heretics. First, the townspeople would be gathered in a public place. Although attendance was voluntary, those who failed to show would automatically be suspect, so most would come. The inquisitors would provide an opportunity for anyone to step forward and denounce themselves in exchange for easy punishment. As part of this bargain they would need to inform on other heretics. In addition, the inquisitors could simply force people to be interrogated. Once information had been gathered, an inquisitorial trial could begin.
Trial
The inquisitorial trial generally favored the prosecution (the Church). The defendant would be allowed a lawyer, but if the defendant was convicted, the lawyer would lose his ability to practice. Therefore most lawyers never took the chance of defending a potential heretic. The trials were conducted in secret with only the inquisitors, the defendant and some inquisitorial staff to take notes. Inquisitors sequestered all of the property of the defendant. The defendant was not told the charges, but was always invited to confess, only guessing what for. The accused was expected to self-incriminate and did not have the right to face and question the accuser. It was acceptable to take testimony from criminals, persons of bad reputation, excommunicated people, and convicted heretics. Blood relationship did not exempt one from the duty to testify against the accused. Sentences could not be appealed once made. The inquisitor could keep a defendant in prison for years before the trial to obtain new information.
Despite the seeming unfairness of the procedures, the inquisitors did provide rights to the defendant. At the beginning of the trial, defendants were invited to name those who had "mortal hatred" against them. If the accusers were among those named, the defendant was set free and the charges dismissed; the accusers would face life imprisonment. This option was meant to keep the inquisition from becoming involved in local grudges. A confession under torture was not admissible in court, although the inquisitor could threaten the accused with torture during the proceedings.
Torture
Torture was used after 1252. On May 15, Pope Innocent IV issued a papal bull entitled Ad exstirpanda, which authorized the use of torture by inquisitors. It was a common part of the medieval judicial system and not particular to the inquisition. The torture methods used by inquisitors were mild compared to secular courts, as they were forbidden to use methods that resulted in bloodshed, mutilation or death. Also, torture could be performed only once (although a session could be "suspended", and when continued would be regarded as the same session of torture). One of the more common forms of medieval inquisition torture was known as strappado. The hands were bound behind the back with a rope, and the accused was suspended this way, dislocating the joints painfully in both arms. Weights could be added to the legs dislocating those joints as well.
Punishment
Once the trial was concluded the results might take years to be revealed, during which time the defendant stayed in prison. The inquisitors would save up the cases and announce them at once in a public ceremony called, in Latin, sermo generalis, or "general sermon." Among the possible punishments were a long pilgrimage for first offenders, wearing a yellow cross for life, confiscation of property, banishment, public recantation, or long-term imprisonment. Burning at the stake was only for the most serious cases, including repeat offenders and unrepentant heretics. Execution was done not by the Church, which was forbidden to kill, but by secular officials. The accused could have all of his property confiscated, and in many cases, accusers may have been motivated by a desire to take the property of the accused.
The inquisitors generally preferred not to hand over heretics to the secular arm for execution if they could persuade the heretic to repent. It was in the inquisitors' interest to be perceived as merciful, and they generally preferred to keep defendants alive in hopes of obtaining confessions. For example, Bernard Gui, a famous inquisitor working in the area of Toulouse (in modern France), executed 42 people out of over 900 guilty verdicts in fifteen years of office. Execution was to admit defeat, that the Church was unable to save a soul from heresy, which was the goal of the inquisition.