About Boniface, Alexander VI (r. 1492-1503),  Benedict IX and John XII (r. 955-964) the evidence is less certain.

Among the early popes who notable tolerated or protected people accused of homosexual practices, we should remember Pope Callistus, who was harshly criticized by Tertullian for his failure to condemn sex between men; Pope Leo IX, who implemented many of St Peter Damian‘ s proposals for church reform, but rejected the appeals for harsh penalties against clerical “sodomites”, and also rejected appeals to prevent the consecration as bishop of the promiscuous John (or Jean) of Orleans. Later, ,Paul III (1534 -49) is said to have protected and bestowed honours on his son, Pier Luigi Farnese, who surrounded himself with male lovers, used Roman police to track down a young man who had spurned his advances, and was accused of raping a bishop and other clerics.

A passage from the glbtq.com is fascinating for the very different picture it paints to that prevailing elsewhere, at a time when the inquisition and secular powers were burning between them thousans of men across Europe and in the New World:…

Nor was he the only cleric who enjoyed some male company.  Here’s Saslow again:

The intimate living arrangements of the all-male clerical world and the opportunities that educational and religious duties afforded for privacy and empiotional intimacy, while not themselves “causes” of of homosexuality, may have contributed circumstantially to their expression.  Priests in fifteenth century Venice and Stuart Sussex were convicted of sex with young parishioners, unpublished records of church trials in Loreto, Italy, in the 1570’s detail the activities of a choirboy who slept successively with various older monks……

http://queerhistory.blogspot.in/2010/03/gay-popes-embarrassing-death-of-paul-ii.html

List of Sexually Active Popes.

Sexually active after receiving Holy Orders

• Pope Julius II (1503–1513) had at least one illegitimate daughter, Felice della Rovere (born in 1483, twenty years before his election). Some sources indicate that he had two additional illegitimate daughters, who died in their childhood.^[18] Furthermore, some (possibly libellous) reports of his time accused him of sodomy. According to the schismatic Council of Pisa in 1511, he was a “sodomite covered with shameful ulcers.”^[19]
• Pope Paul III (1534–1549) held off ordination^[20] in order to continue his promiscuous lifestyle, fathering four illegitimate children (three sons and one daughter) by his mistress Silvia Ruffini. He broke his relations with her ca. 1513. There is no evidence of sexual activity during his papacy.^[21] He made his illegitimate son Pier Luigi Farnese the first Duke of Parma.^[22][23]
• Pope Pius IV (1559–1565) had three illegitimate children before his election to the papacy.^[24]

[edit]Sexually active during their pontificate

• Pope Sergius III (904–911) was supposedly the father of Pope John XI by Marozia, according to Liutprand of Cremona in his Antapodosis,^[25] as well as the Liber Pontificalis.^[26] However, this is disputed by another early source, the annalist Flodoard (c. 894-966), John XI was brother of Alberic II, the latter being the offspring of Marozia and her husband Alberic I. Hence John too may have been the son of Marozia and Alberic I. Bertrand Fauvarque underlines that the contemporary sources backing up this parenthood are dubious, Liutprand being “prone to exaggeration” while other mentions of this fatherhood appear in satires written by supporters of late Pope Formosus.^[27]
• Pope John X (914–928) had romantic affairs with both Theodora and her daughter Marozia, according to Liutprand of Cremona in his Antapodosis:^[28] “The first of the popes to be created by a woman and now destroyed by her daughter”. (See also Saeculum obscurum)
• Pope John XII (955–963) (deposed by Conclave) was said to have turned the Basilica di San Giovanni in Laterano into a brothel and was accused of adultery, fornication, and incest (Source:Patrologia Latina).^[29] The monk chronicler Benedict of Soracte noted in his volume XXXVII that he “liked to have a collection of women”. According to Liutprand of Cremona in hisAntapodosis,^[25] “they testified about his adultery, which they did not see with their own eyes, but nonetheless knew with certainty: he had fornicated with the widow of Rainier, with Stephana his father’s concubine, with the widow Anna, and with his own niece, and he made the sacred palace into a whorehouse.” According to The Oxford Dictionary of Popes, John XII was “a Christian Caligula whose crimes were rendered particularly horrific by the office he held”.^[30] He was killed by a jealous husband while in the act of committing adultery with the man’s wife.^{[31][32][33][34]} (See also Saeculum obscurum)
• Pope Benedict IX (1032– became pope in 1044, again in 1045 and finally 1047–1048).^[35] He was accused by Bishop Benno of Piacenza of “many vile adulteries.”^[36][37] Pope Victor III referred in his third book of Dialogues to “his rapes… and other unspeakable acts.”^[38] His life prompted St. Peter Damian to write an extended treatise against sex in general, and homosexuality in particular. In his Liber Gomorrhianus, Damian accused Benedict IX of routine sodomy and bestiality and sponsoring orgies.^[39] In May 1045, Benedict IX resigned his office to pursue marriage.^[40]

http://en.wikipedia.org/wiki/List_of_sexually_active_popes

 

http://www.dailymail.co.uk/news/article-2253046/Pope-uses-Christmas-Mass-ask-people-room-God-technology-driven-lives.html