I'd contest that referring to someone as a "crusader" is necessarily positive - it also has connotations of zealotry and a very negative single-mindedness to the exclusion of reason in the modern context, but as you say, you want to judge for yourself. My knowledge of the Inquisitions is surface at best, so I'll leave that for another poster to address and make some notes on the Crusaders.

What portion of soldiers in the historical crusades were complicit in the sacks/pogroms in Europe?

It varies depending on which Crusade you look at, but the First and Fourth are most famous for this behaviour. In the First Crusade, relatively few Crusaders participated. The offenders were an absolutely ragtag group of pilgrims who were mostly utterly impoverished peasants who constituted what's called the People's Crusade. The whole thing was an absolute disaster. Their soldiers were peasants stirred up into a religious fervour by the movement's leader, Peter the Hermit, who was acting somewhat independently of either the secular or religious authorities directing the First Crusade. He intended to (and did, eventually) lead his Crusaders from France through Germany to Byzantium and then be ferried across to the recently lost holdings in northern Turkey to start Crusading.

That's essentially what happened. But along the way, his troops started massacring Jews. The 'why' of that is an open question. Some have argued that it was an extension of the religious zeal that motivated many Crusaders - they didn't see the point in going to the Holy Land to fight infidels when, in their view, Christ's murderers were already living among them in Europe. Others propose it was purely for economic gain. Jews had a (somewhat earned) reputation as wealthy, often usurers or merchants with a fair bit of wealth, and the largely poor Crusaders saw an opportunity for plunder that wasn't likely to be very heavily contested by their fellow Christians.

It wasn't, either. Some cities, whether because of their community relationships with the Jews or because of specific acts of protection undertaken by local bishops or nobles protected their Jews. Many others, however, heard what was happening as the People's Crusade made its way across Europe and either opened their gates to turn their Jews over to the Crusaders or, in more extreme cases, simply had pogroms and looted them themselves, occasionally despite a promise of protection from local authorities.

Eventually the People's Crusade made its way to Byzantium, was ferried to Turkey as quickly as possible by Alexius Komnenus, who wanted them out of his city ASAP, and were promptly slaughtered by Kilij Arslan, the Seljuq prince of the lands bordering Byzantium that had recently been conquered by the Seljuqs. The rest of the First Crusade arrived months later, led by both military and spiritual leaders of much higher standing and respect than Peter the Hermit or his military counterpart, Walter the Penniless, and with official papal backing. They conducted themselves much more professionally in their march across Europe.

The Fourth Crusade is its own whole confusing thing. Suffice to say that the Crusading army intended to march on Egypt, ran out of money, cut a few deals to help initiate a coup in Byzantium for more funding to get to Egypt, then when that deal fell through decided to cut their losses and sack Byzantium in an effort to come away somehow better off for it. There's no real "good guys" in that story - pretty much everybody who was part of that Crusade participated in the sack of Byzantium.

Was crusader warfare in the Middle East war-as-usual for the time, or did it cross lines usual in intra-Europe warefare?

I confess I don't have a great enough knowledge of intra-European warfare to give this the full answer it deserves. I will tell you, however, that the warfare the Crusaders waged in the Holy Land was absolutely brutal. The Muslim chronicles especially of some of the early battles are absolutely horrified. A good early example of this is the Battle of Ma'arra, where the Crusaders, low on supplies, frantically captured the city and proceeded to massacre everyone inside (relatively common in some of the early captures, but a fate most major cities avoided and a less common phenomenon as the Crusade dragged on), only to discover that the city had much less food than anticipated. Waylaid by winter and disputes among their leadership (a common problem for the Crusaders), they eventually resorted to eating the bodies of the massacred Muslim population.

The sack of Jerusalem was pretty heinous - lots of massacres there, including of prisoners who had already been guaranteed safeties (often as a result of the infighting amongst the Crusade's leadership). In this sack, as in most of the battles fought in the Crusades, religious affiliation was no guarantee of mercy. The Muslims were the Crusaders' main focus, but Jews in Jerusalem and throughout the Holy Land were not seen as much better, and even Coptic and Armenian Christians were rarely differentiated once battle was joined. The Armenian Christians would in fact usually fight on the Muslim side, especially during sieges - if, that is, the Muslim leaders allowed them to remain. The Armenian Christians were caught between a rock and a hard place in a lot of the Crusades, both alien to the Catholic Crusaders and mistrusted by the Muslims who didn't differentiate between Christians. But yeah, war in the Holy Land was pretty merciless and involved a lot of massacres, especially in the early days.

Are there notable historic examples of Crusaders or Inquisitors doing good that should not be forgotten, just as we should not forget the bad behavior?

This is a little bit tougher. I'm going to look at it from a modern view of morality (see this good discussion on making moral judgements about the past, a topic well worth consideration in your question), and a lot of what happened in the Crusades was pretty morally despicable from our point of view. Moreover, some romanticizing of the Crusades in days gone by means that a good deal of historiography focuses on dispelling that mythology, rather than bringing laudable behaviour to the forefront. That said, there are two things that come to mind.

First, the Crusader kingdoms set up after the conquest of Jerusalem, the Latin States, established gender-neutral primogeniture. Baldwin II, third King of Jerusalem, was something of a radical feminist by the standards of his day. He reportedly postponed his own coronation as King of Jerusalem so that his wife could be crowned alongside him, and when it became clear to him that his days were growing few, he took measures to circumvent the European tradition of male-only inheritance to ensure that his eldest daughter, Melisende, would inherit his throne, a position he had raised her to one day assume. This established a precedent that persisted as long as the Latin States did.

The other is the knightly orders. These are most commonly remembered as military orders, and rightly so as that would ultimately become their primary function. However, two of the Big 3 orders, the Hospitallers and the Teutonic Knights, started out as monastic hospitals, and quite charitable ones at that. They initially served as medics after battles, and not necessarily just for Christians (though obviously they dealt with them primarily). They also ensured safe passage for peaceful pilgrims without affiliation to the Crusades to Jerusalem. This isn't anything hugely philanthropic, but it is a side of the Crusade less examined - the relatively peaceful practice of faith that was achieved in the inter-Crusade periods.

It's also worth noting that once the Latin States were established and consolidated, they weren't all that obtrusive in regional dynamics or politics. When there weren't Crusades happening actively, they were readily comparable to their Muslim neighbours and predecessors. In fact, they became so mired in regional politics that they would often war against each other in participation with spats between Muslim rulers with roots that went much further back then the Crusades.

Edit: This came out quite a bit longer than I anticipated and though this is a survey from memory I feel I should give you some sources on this.

• The Crusades Through Arab Eyes, Amin Maalouf. The /r/AskHistorians recommendation of choice. Invaluable to get a sense of things from the Muslim perspective. Consider also looking into the works of contemporary Muslim chroniclers Ibn al-Athir and Ibn al-Qalanisi, both of whose works on the Crusades are readily available in translation.

• The Crusades, Hans Eberhard Mayer. A solid academic survey of the Crusades, though I personally find him a little generous to the Crusaders.

• The New Cambridge Medieval History vol. 4, David Luscombe and Jonathan Riley-Smith, editors. If you're a university student, your institution probably has online access to a lot of the Cambridge histories, including this one. These are invaluable academic surveys of innumerable subjects. Here's the DOI for the chapter on the Latin East, also by Hans Eberhard Mayer: http://dx.doi.org/10.1017/CHOL9780521414111.025

• European Jewry and the First Crusade, Robert Chazan. Focused on the Jewish experience specifically, this will probably be of the greatest interest to you regarding the pogroms that happened in France and Germany in the early First Crusade.