Summary Answer:For a list of the top ten hateful verses in the Qur'an see here.
The Qur'an contains at least 109 verses that call Muslims to war with nonbelievers for the sake of Islamic rule. Some are quite graphic, with commands to chop off heads and fingers and kill infidels wherever they may be hiding. Muslims who do not join the fight are called 'hypocrites' and warned that Allah will send them to Hell if they do not join the slaughter.
Unlike nearly all of the Old Testament verses of violence, the verses of violence in the Qur'an are mostly open-ended, meaning that they are not restrained by the historical context of the surrounding text. They are part of the eternal, unchanging word of Allah, and just as relevant or subjective as anything else in the Qur'an.
The context of violent passages is more ambiguous than might be expected of a perfect book from a loving God, however this can work both ways. Most of today's Muslims exercise a personal choice to interpret their holy book's call to arms according to their own moral preconceptions about justifiable violence. Apologists cater to their preferences with tenuous arguments that gloss over historical fact and generally do not stand up to scrutiny. Still, it is important to note that the problem is not bad people, but bad ideology.
Unfortunately, there are very few verses of tolerance and peace to abrogate or even balance out the many that call for nonbelievers to be fought and subdued until they either accept humiliation, convert to Islam, or are killed. Muhammad's own martial legacy - and that of his companions - along with the remarkable stress on violence found in the Qur'an have produced a trail of blood and tears across world history. LINK.