http://askville.amazon.com/people-killed-Inquisition/AnswerViewer.do?requestId=3878676
According to public news reports the book's editor, Prof. Agostino Borromeo, stated that about 125,000 persons were investigated by the Spanish Inquisition, of which 1.8% were executed (2,250 people).
During the high point of the Spanish Inquisition from 1478-1530 AD, scholars found that approximately 1,500-2,000 people were found guilty. From that point forward, there are exact records available of all "guilty" sentences which amounted to 775 executions. In the full 200 years of the Spanish Inquisition, less than 1% of the population had any contact with it, people outside of the major cities didn't even know about it. The Inquisition was not applied to Jews or Moslems, unless they were baptised as Christians.
If we add the figures, we find that the entire Inquisition of 500 years, caused about 6,000 deaths.
That's the inquisition... now more generally.. you probably want this:
http://www.truthbeknown.com/victims.htm
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Now I'm skipping some of what I consider dubious examples where a war between nations is less strongly associated with religion than with a conflict between the people but it's fair to say that religion (the catholic/christian religion) was a factor to a major factor in these conflicts.
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Emperor Karl (Charlemagne) in 782 had 4500 Saxons, unwilling to convert to Christianity, beheaded. [DO30]
Peasants of Steding (Germany) unwilling to pay suffocating church taxes: between 5,000 and 11,000 men, women and children slain 5/27/1234 near Altenesch/Germany. [WW223]
Jerusalem conquered 7/15/1099 more than 60,000 victims (jewish, muslim, men, women, children). [WW37-40]
(In the words of one witness: "there [in front of Solomon's temple] was such a carnage that our people were wading ankle-deep in the blood of our foes", and after that "happily and crying for joy our people marched to our Saviour's tomb, to honour it and to pay off our debt of gratitude")
The Archbishop of Tyre, eye-witness, wrote: "It was impossible to look upon the vast numbers of the slain without horror; everywhere lay fragments of human bodies, and the very ground was covered with the blood of the slain. It was not alone the spectacle of headless bodies and mutilated limbs strewn in all directions that roused the horror of all who looked upon them. Still more dreadful was it to gaze upon the victors themselves, dripping with blood from head to foot, an ominous sight which brought terror to all who met them. It is reported that within the Temple enclosure alone about ten thousand infidels perished." [TG79]
Battle of Askalon, 8/12/1099. 200,000 heathens slaughtered "in the name of Our Lord Jesus Christ". [WW45]
1391 Seville's Jews killed (Archbishop Martinez leading). 4,000 were slain, 25,000 sold as slaves. [DA454] Their identification was made easy by the brightly colored "badges of shame" that all jews above the age of ten had been forced to wear.
1572 In France about 20,000 Huguenots were killed on command of pope Pius V. Until 17th century 200,000 flee. [DO31]
Albigensians: the first Crusade intended to slay other Christians. [DO29]
The Albigensians...viewed themselves as good Christians, but would not accept roman Catholic rule, and taxes, and prohibition of birth control. [NC]
Begin of violence: on command of pope Innocent III (greatest single pre-nazi mass murderer) in 1209. Bezirs (today France) 7/22/1209 destroyed, all the inhabitants were slaughtered. Victims (including Catholics refusing to turn over their heretic neighbours and friends) 20,000-70,000. [WW179-181]
As one of the culprits wrote: "So many Indians died that they could not be counted, all through the land the Indians lay dead everywhere. The stench was very great and pestiferous." [SH69]
The indian chief Hatuey fled with his people but was captured and burned alive. As "they were tying him to the stake a Franciscan friar urged him to take Jesus to his heart so that his soul might go to heaven, rather than descend into hell. Hatuey replied that if heaven was where the Christians went, he would rather go to hell." [SH70]
What happened to his people was described by an eyewitness:
"The Spaniards found pleasure in inventing all kinds of odd cruelties ... They built a long gibbet, long enough for the toes to touch the ground to prevent strangling, and hanged thirteen [natives] at a time in honor of Christ Our Saviour and the twelve Apostles... then, straw was wrapped around their torn bodies and they were burned alive." [SH72]
Or, on another occasion:
"The Spaniards cut off the arm of one, the leg or hip of another, and from some their heads at one stroke, like butchers cutting up beef and mutton for market. Six hundred, including the cacique, were thus slain like brute beasts...Vasco [de Balboa] ordered forty of them to be torn to pieces by dogs." [SH83]
The "island's population of about eight million people at the time of Columbus's arrival in 1492 already had declined by a third to a half before the year 1496 was out." Eventually all the island's natives were exterminated, so the Spaniards were "forced" to import slaves from other caribbean islands, who soon suffered the same fate. Thus "the Caribbean's millions of native people [were] thereby effectively liquidated in barely a quarter of a century". [SH72-73] "In less than the normal lifetime of a single human being, an entire culture of millions of people, thousands of years resident in their homeland, had been exterminated." [SH75]
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But this was all in the distance past. Probably nothing like that in the last 100 years.
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20th Century Church Atrocities
Catholic extermination camps
Surpisingly few know that Nazi extermination camps in World War II were by no means the only ones in Europe at the time. In the years 1942-1943 also in Croatia existed numerous extermination camps, run by Catholic Ustasha under their dictator Ante Paveli, a practising Catholic and regular visitor to the then pope. There were even concentration camps exclusively for children!
In these camps - the most notorious was Jasenovac, headed by a Franciscan friar - orthodox-Christian serbians (and a substantial number of Jews) were murdered. Like the Nazis the Catholic Ustasha burned their victims in kilns, alive (the Nazis were decent enough to have their victims gassed first). But most of the victims were simply stabbed, slain or shot to death, the number of them being estimated between 300,000 and 600,000, in a rather tiny country. Many of the killers were Franciscan friars. The atrocities were appalling enough to induce bystanders of the Nazi "Sicherheitsdient der SS", watching, to complain about them to Hitler (who did not listen). The pope knew about these events and did nothing to prevent them. [MV]
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Well-- nothing like that in the last 65 years!
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Well if we count the 1990's rwandan catholic priests as lone gunmen, then certainly not.
(tho I'll grant there was a lot of ethnic conflict mixed in with that one. I really do picture those catholic murderers as not acting with the backing of the church).