We’re fortunate to have quite a lot of information about how the First Crusade was organized in 1095/1096 - basically, the pope sent letters and preachers to other parts of Europe to spread the message, and it was agreed that everyone should leave on August 15, 1096. After that the level of organization was a bit vague. They were supposed to meet up in Constantinople, eventually, and so they did, either by land or by sea, in November and December. A lot people didn’t wait - the "peoples" crusade" arrived in Constantinople much earlier, and they were all shipped off across the Bosporus to Anatolia where they were mostly killed. The main wave of the crusade was also ferried across to Anatolia as soon as feasible, early in 1097.
For pilgrimages prior to the First Crusade, we really don’t have the same amount of information. Large groups of pilgrims probably organized themselves by sending letters and agreeing on a departure date, just like the crusaders did. We don’t actually know for sure, but it’s likely that the crusade was organized using the same methods as previous pilgrimages, since those methods had already proven to be successful.
There were pilgrimages to Jerusalem long before the crusade, going back to the 4th century when the Roman Empire was Christianized, and they continued even after Jerusalem was part of Muslim territory. There were still Orthodox and other eastern Christians there, and they may have even been the majority of the population for centuries after the Muslim conquest. The emperor in Constantinople considered himself to be the special protector of the eastern Christians, and he paid for the maintenance and construction of churches. Sometimes the situation in Jerusalem wasn’t safe for native Christians or pilgrims, for example when the Fatimid caliph of Egypt, al-Hakim, destroyed the Church of the Holy Sepulchre in Jerusalem in 1009.
Despite al-Hakim’s persecution, pilgrims continued to arrive from Europe. Just before this, in 1003, Count Fulk III of Anjou travelled to Jerusalem, and he went back again in 1011, after the Sepulchre was destroyed. Pilgrimages were a bit easier and safer again after Al-Hakim died in 1021. Viscount Guy of Limoges went on pilgrimage around 1025, Count William II of Angouleme travelled there in 1026, and Fulk of Anjou returned again along with Duke Robert I of Normandy in 1035. These were small, individual pilgrimages though, and probably easier to organize than a mass movement.
These names might sound familiar, because their descendants also participated in the First Crusade or in pilgrimages in the early years after the crusade. Robert I’s grandson Robert II was one of the leaders of the crusade, and Fulk III’s great-grandson Fulk V became king of Jerusalem in 1131. So, while the First Crusade was something new and unusual, it didn’t appear out of nowhere - there were already existing pilgrimage traditions in crusader families.
As for mass pilgrimages, there was a famous one in 1064/65, only 30 years before the crusade. The sources for this pilgrimage don’t really tell us anything about how it was organized, just that some German bishops (including Siegfried of Mainz, William of Utrecht, Otto of Regensberg, and Gunther of Bamberg) organized it with
“a great multitude of counts and princes, rich and poor, apparently greater than twelve thousand in number” (Whalen, pg. 175).
They walked to Constantinople through Hungary and Bulgaria, just as the French pilgrims had done earlier in the century, and as the crusaders did a generation later. They continued to Latakia, then reached Tripoli, where the emir tried to intercept and kill them, but he was stopped by a miraculous storm. Near Jerusalem they were attacked by Muslim bandits, but the Fatimid governor rescued them,
“for he figured that if all of these men perished in such a great slaughter, then no one else would come to the land for the sake of prayer, and therefore he and his men would incur a great loss of revenues.” (Whalen, pg. 178)
The pilgrims visited Jerusalem for a couple of weeks before sailing back home, rather than walking.
So, we don’t really know how pilgrimages were organized pre-crusade, but the crusade was part of a long tradition of pilgrimages to Jerusalem. Presumably, the crusade was organized based on the way that earlier pilgrimages had been organized.
Sources:
Einar Joranson, “The Great German Pilgrimage of 1064-1065”, in The Crusades and Other Historical Essays , ed. Louis J. Paetow (New York, 1928)
Daniel F. Callahan, Jerusalem and the Cross in the Life and Writings of Ademar of Chabannes (Brill, 2016), particularly the chapter “Jerusalem Pilgrims from the West Frankish Kingdom in the Tenth and Early Eleventh Centuries in Ademar’s Writings”
Brett Whalen, Pilgrimage in the Middle Ages: A Reader (University of Toronto Press, 2011), in particular No. 38 (“The German Pilgrimage of 1064-65), pg. 175-179
Bernard S. Bachrach, Fulk Nerra, the Neo-Roman Consul (University of California Press, 1993)