The Quran contains at least 109 verses that speak of war with nonbelievers, usually on the basis of their status as non-Muslims. 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, most verses of violence in the Quran are open-ended, meaning that they are not necessarily restrained by historical context contained in the surrounding text (although many Muslims choose to think of them that way).
They are part of the eternal, unchanging word of Allah, and just as relevant or subject to interpretation as anything else in the Quran.
The context of violent passages is more ambiguous than might be expected of a perfect book from a loving God. Most contemporary Muslims exercise a personal choice to interpret their holy book's call to arms according to their own moral preconceptions about justifiable violence. Islam's apologists cater to these preferences with tenuous arguments that gloss over historical fact and generally don't 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 balance out those calling for nonbelievers to be fought and subdued until they either accept humiliation, convert to Islam, or are killed. Muhammad's own martial legacy, along with the remarkable emphasis on violence found in the Quran, have produced a trail of blood and tears across world history.
Quran (2:216) - "Fighting is prescribed for you, and ye dislike it. But it is possible that ye dislike a thing which is good for you, and that ye love a thing which is bad for you. But Allah knoweth, and ye know not." Not only does this verse establish that violence can be virtuous, but it also contradicts the myth that fighting is intended only in self-defense, since the audience was obviously not under attack at the time. From the Hadith, we know that this verse was narrated at a time that Muhammad was actually trying to motivate his people into raiding merchant caravans for loot. (See also: Response to Apologists)
Quran (3:56) - "As to those who reject faith, I will punish them with terrible agony in this world and in the Hereafter, nor will they have anyone to help." (See also: Response to Apologists)
Quran (3:151) - "Soon shall We cast terror into the hearts of the Unbelievers, for that they joined companions with Allah, for which He had sent no authority". This speaks directly of polytheists, yet it also includes Christians, since they believe in the Trinity (ie. what Muhammad incorrectly believed to be 'joining companions to Allah'). (See also: Response to Apologists)
Quran (4:74) - "Let those fight in the way of Allah who sell the life of this world for the other. Whoso fighteth in the way of Allah, be he slain or be he victorious, on him We shall bestow a vast reward." The martyrs of Islam are unlike the early Christians, who were led meekly to the slaughter. These Muslims are killed in battle as they attempt to inflict death and destruction for the cause of Allah. This is the theological basis for today's suicide bombers. (See also: Response to Apologists)
Quran (4:76) - "Those who believe fight in the cause of Allah…"
Quran (4:89) - "They but wish that ye should reject Faith, as they do, and thus be on the same footing (as they): But take not friends from their ranks until they flee in the way of Allah (From what is forbidden). But if they turn renegades, seize them and slay them wherever ye find them; and (in any case) take no friends or helpers from their ranks." (See also: Response to Apologists)