There was a journal called Kerem Chemed published in Vienna in the 1830s through 1850s. In volume 5, there was an article by Leopold Zunz about Azariah de Rossi and his controversial book Me'or Einayim. The book was considered heretical by many, was about to be banned by R. Yosef Karo (the author of Shulchan Arukh) when he died, and was harshly denounced by the Maharal (on this episode, see Reuven Bonfil's introduction to his edition of Me'or Einayim). In this article, Zunz listed a number of respected authors who freely quote from Me'or Einayim. Volume 7 has a follow-up article by Zunz in which he responds to a very detailed critique he received from R. Matisyahu Strashoun. R. Strashoun, the son of the Rashash, was a wealthy bibliophile in Vilna whose glosses on the Talmud, along with his father's, are published in the standard Vilna edition of the Talmud (no doubt partly due to his wealth). From Zunz's response, it is clear that R. Strashoun was intimately familiar with Me'or Einayim.
Zunz quotes the following sources that cite Me'or Einayim (note that this is just a subset of his list):
- R. David Ganz, the famous student and successor of the Maharal(!), in his Tzemach David, vol. 1 pp. 7, 19,...; vol. 2 pp. 9b, 11a; Nechmad Ve-Na'im, no. 90.
- Tosafos Yom Tov (also a student of the Maharal!), Menachos 10:3
- Minchas Shai, Zekhariah 14:5
- R. Yosef Shlomo Delmedigo, Matzref Le-Chokhmah 8b; Novelos Chokhmah 111a; Mikhtav Achuz p. 22
- Yedei Moshe on Bereshis Rabba ch. 46. R. Matisyahu Strashoun suggests that this is really a reference to Mosaf Arukh and not Me'or Einayim.
- Chavos Ya'ir, no. 9. R. Matisyahu Strashoun suggests that this refers to Ba'al Ha-Ma'or and not Me'or Einayim. However, here is how it looks in the 1997 Eiked Sefarim edition:
The Greek chief of philosophers said: "Love Socrates; love Plato; only the truth love more." This is brought in Nishmas Chaim, essay 2 ch. 10; Me'or Einayim, Imrei Binah ch. 48; Ba Gad, ch. 4; the introduction to Chozek Ha-Emunah, the introduction to Sefer Ha-Emunos and other places. The Rivash wrote similarly in responsum 370.I'm not sure if this is different from what R. Strashoun saw and emended.
- R. Yishayahu Basan, Lachmei Todah, no. 19
- R. Yitzchak Lampronti, Pachad Yitzchak, sv. kelayos 72b
- R. Elazar Fleckeles, Melekhes Ha-Kodesh 2:3
- Otzar Nechmad on Kuzari, introduction
- R. Tzvi Hirsch Chajes, Toras Nevi'im, 7b
- R. Yishayahu (Pik) Berlin, Minei Targima, likkutim at the end
Also, about a year ago I had a discussion about this with Gil Perl, who is writing his doctoral dissertation on the Netziv. He said that the Netziv (R. Naphtali Tzvi Yehudah Berlin) quotes Me'or Einayim in six places: once in his Ha'amek Davar commentary (Ex. 28:36) and five times in his commentary to Sifrei. Perl also said that there is a clear and pervasive influence of Me'or Einayim throughout the commentary to Sifrei, but I'd guess that this is an evaluation that those who wish to can dispute (link).
THE POINT of all this is that the above authors either disagreed with the condemnations of Me'or Einayim or felt that even a forbidden, and perhaps heretical, book may be studied and quoted (see this post). R. Chajes was clearly of the former view, since he consistently refers to the author of Me'or Einayim as "Ha-Rav." I'm not too sure about the others.
UPDATE: A commenter pointed out, and I verified, that R. Moshe Sofer quotes Me'or Einayim in his Responsa Chasam Sofer, vol. 5, hashmatos 193. Note that this is a letter to R. Ephraim Zalman Margoliyos whom R. Sofer assumed would not object to the quotation.