Who has not made me a gentile
In the manuscripts of the Babylonian Talmud, Menachot 43b, we read,
Rabbi Yehudah  would say: A person is obligated to recite the following three blessings every day-[Praised are you...] who has not made me a Gentile (גוי); who has not made me a woman (אשה); [*] who has not made me an ignoramous (בור).
Yet if one looks in the Vilna edition of the Talmud and many of those based upon this edition, instead of reading that one should bless “who has not made me a Gentile”, it says “who has made me an Jew/Israelite (שעשני ישראל). These words are in parentheses, signifying that they should be altered. It was obvious to many that the blessing “who has not made me a Gentile” was changed in order not to offend non-Jews. This blessing is also found in most traditional prayer books and through an examination of mss. of prayer books and earlier printed editions, one can also see the interesting history of this blessing. In some prayer books the blessing is found, yet it is crossed out. In others the blessing, as with the other two, is presented in contrasting terms: e.g. thanking God for making me a Jew but not a Gentile, or in one version an Ishmaelite. Others either don’t contain it at all, or have altered it to thanking God for making me a Jew (ישראל). The latter option being adopted by the prayer books of the Conservative Movement since the middle of the 20th century.
It is not only in prayer books that one can follow the textual history of this blessing, but also in halakhic codes such as the Shulhan Aruch. In some editions of the SA it says that in the morning one should recite the blessing “who has made me a Jew/ישראל”, while in others it says “who has not made me a Gentile/גוי or עובד כוכבים” (OH 46:4). In the first edition (1565) of the SA the text reads “who has not made me a Gentile/גוי”, and already in the later Krakow edition (1578) it was changed to “who has made me a Jew”. Is this an anti-Gentile blessing? Saul Lieberman in his Tosefta ke-Peshuta (p. 120) bring a number of scholars who have noted that the formulation of a blessing in the negative was common in the antiquity, bringing a quote from someone who offered praise that he was born a man and not an animal, a male and not a female, and a Hellenist and not a barbarian. That Lieberman tries to justify the formulation of the blessing within its historical context, shows its problematic nature.
 In one mss. this is brought in the name of Rabbi Meir, but since both the Tosefta (Berachot 6:18) and the Yerushalmi have Rabbi Yehudah, he is most likely the correct tradent.
[*] The versions of the blessing in prayer books that have women thanking God for making them a woman and not a man is also quite fascinating.
Sources: See Naphtali Weider’s article “Al ha-Berachot ‘Goy-Eved-Ishah’, ‘Beheima’ ve-’Bor‘” which was reprinted in his collected studies, Hitgabshut Nusah ha-Tefillah, and R. Yitzhak Nissim’s article “Hagahot al ha-Shulhan Aruch” in the book Rabbi Yosef Karo, published by Mossad haRav Kook in 1969.