This Disunion piece talks about one case that Lincoln refused to pardon (rightfully so, in my opinion), but spends just as much time discussing his liberal application of the clemency right. To me, this is one of Lincoln’s most endearingly humane qualities.
There were three areas in which Lincoln’s pardoning power could be applied. The first related to cases in the civil courts. During his tenure, Lincoln reviewed 456 civil cases; 375 of them – over 82 percent — received pardons. The second class had to do with those in rebellion against the government. This being the Civil War, more than half the country qualified.
The third category was in military cases. It was here that Lincoln received the most criticism for what was perceived as his interference in the flow of military justice and discipline. He made it clear from the beginning that he was “unwilling for any boy under 18 to be shot,” and he had a tendency to pardon youths who had fallen asleep on guard duty or had deserted. Gen. Joseph Hooker once sent an envelope to the president containing the cases of 55 convicted and doomed deserters; Lincoln merely wrote “Pardoned” on the envelope and returned it to Hooker.