Good question! I apologize in advance if this turns out to be long answer. Caesar lived in a brutal and dangerous era. During most of his lifetime the dangers that came with with public life were higher than ever. The higher a man rose and the greater the risks he took the harder the fall was likely to be. By the time Caesar was a grown man the spectre of a military dictatorship was nothing new, he grew up with mass massacres of the senate and nearly became a victim himself.

Young arisocrats like Caesar who follow their fathers during daily business were raised to aspire to virtus, an important part of which was the absolute resolution to never give in even in the face of defeat. This had served the Republic in earlier wars with Hannibal and Pyrrhus, who couldn't understand why the Romans wouldn't give up when they were so obviously beaten. But when the civil wars came this made sure that they were waged with absolute ruthlessness. The leading men knew that they had to win or die. It was very rare for generals to commit suicide when faced with defeat in a foreign war because it was their job to rebuild and fight on when they were strong enough. In civil wars however the regular soldiers could expect mercy upon defeat, but the leaders could not.

This lead to many rebel leaders commiting suicide en masse wether it was in despair or defiance (suicide was in this age seen as a brave and honorable way to go out). Caesar tried to change this. When Brutus and Cicero surrendered themselves to Caesar they expected to be executed as had happened in earlier civil wars. Caesar spared them. Although they kept their lives, from their point of view this was most humiliating, and they would be mocked for the rest of their careers.

When the war began Caesar paraded his clemency by sparing defeated enemies and in time allowing them to continue their careers. This was a calculated move intended to win over uncertain enemies and deter the enemy from fighting to the death. After the war, the defeated pompeians were allowed to continue their public careers and were in fact treated very well. Clearly he thought that this would persuade more senators to accept his dictatorship.

Although we cannot know his motives for sure Caesar generosity is matched by no other Roman who came in power in similar circumstances, and it was not by any means normal. Caesar had during his whole public life campaigned the popular causes, and thus became very popular amongst regular romans. Perhaps one of the reasons for his actions was that he wanted to add to that appeal.

At times Caesar was utterly ruthless, though this was far more seen in his campaigns in Gaul. I do not see really that he acted more merciful or less merciful than any other roman commander would. Vercingetorix the leader of the gauls were sent in chains to Rome to be paraded in his Triumph, as any other roman commander would have done. After his defeat over a million people were enslaved.

Some tribes he treated more lenietly than others. Many tribes were already allies with Rome, providing them when supplies and soldiers. At times he was merciful with some tribes and harsher with others depending on the circumstances.

Source: Caesar by Adrian Goldsworthy

EDIT: Grammar