Which rabbis in the Talmud were placed under cherem (excommunication)? We know about Rabbi Eliezer Bava Metzia 59b and Rabbi Akavia ben Mahalal’el [Eduyyot 7b, but see discussion there]. Anybody else?
Rabbi Eliezer Baba Metzia 59b (as cited in the question)
ונמנו עליו וברכוהו
Then they took a vote and excommunicated him
The Mishna in Ta'anit 3:8 mentions a Hava Amina of Shim'on ben Shatach to make a Cherem or Choni Hameagel.
שָׁלַח לוֹ שִׁמְעוֹן בֶּן שָׁטָח, אִלְמָלֵא חוֹנִי אַתָּה, גּוֹזְרַנִי עָלֶיךָ נִדּוּי.
Simeon, son of Shatach sent him word, "If thou wert not Honee, I would order thee to be anathematised
Akavia Ben Mahalalel or Eleazar Ben Chanoch (machloket tanayim). Eduyot 5:6
.ונדוהו, ומת בנדויו, וסקלו בית דין את ארונו. אמר רבי יהודה, חס ושלום שעקביא נתנדה, שאין עזרה ננעלת בפני כל אדם מישראל בחכמה וביראת חטא כעקביא בן מהללאל. ואת מי נדו, אלעזר בן חנוך שפקפק בטהרת ידים. ..
They excommunicated him, and he died in excommunication, and the Court stoned his coffin. Said Rabbi Yehudah: God-forbid [one should say] that Akavya was excommunicated! For the [Temple] courtyard is never locked for any man of Israel who has wisdom and fear of sin like Akavya the son of Mehalelel [had]. So who did [the Court] excommunicate? It was Elazar the son of Khanoch, who mocked the [laws of] purity of hands.
There is a story in Gittin 7a with "gniva", an Amora who was not good who died after a klala from Rabbi Elazar.
Moed Kattan 17a brings several examples of Talmidei Chachamim who were excommunicated.
There is a No named rabbi whom Rav Yehuda excommunicated because he wasn't acting properly and this led to that Rabbis eventual death.
Reish Lakish also was excommunicated for having excommunicated someone else who took fruit from his field. This is because he should have told the guy to give the fruit back.
- Rav Pappa said in general not to excommunicate Talmidei Chachamim, so if one has to one should excommunicate oneself until releasing that Talmid Chacham from his excommunication. See here
Here is one more, from a minor tractate of the Talmud, Derech Eretz Rabbah, chapter 1:
-Rabbi Yosei ben Taddai of Tiberias said to Rabbi Gamliel: My daughter is forbidden to me, but her mother [my wife] is permitted to me.
-If the daughter of someone who is permitted to me is NOT permitted to me, then all the more reason why the daughter of someone who is NOT permitted to me should NOT be permitted to me. -Now, most mothers are married and are forbidden to me.
-If they are forbidden to me, then so are their daughters.
-Therefore all marriages are forbidden.
Rabban Gamliel then promptly placed him under cherem (excommunicated him): This sort of kal vachomer (a fortiori) argument is permitted, but you may not use it to abrogate a law of the Torah.
An anonymous Rabbi moved from Pumbedita to Bei Kobi, which was forbidden according to Rav Yosef, and was excommunicated.
רב יהודה אמר שמואל כשם שאסור לצאת מארץ ישראל לבבל כך אסור לצאת מבבל לשאר ארצות רבה ורב יוסף דאמרי תרוייהו אפילו מפומבדיתא לבי כובי ההוא דנפק מפומבדיתא לבי כובי שמתיה רב יוסף ההוא דנפק מפומבדיתא לאסתוניא שכיב אמר אביי אי בעי האי צורבא מרבנן הוה חיי
Rav Yehuda said in the name of Shmuel: just as it is forbidden to leave Israel to Babylon, so is it forbidden to leave Babylon to other lands. Raba and Rav Yosef both said that this applies even to moving from Pumbedita to Bei Kobi. There was a case of someone who left Pumbedita for Bei Kobi, and Rav Yosef excommunicated him. Another person left Pumbedita for Astonia, and died. Abaye said, if this scholar had wanted, he could have lived. (Ketubot 111a)
(I left the last lines in the quote to show that the context suggests that this is a discussion specifically about scholars who leave their place of learning.)
Maybe the questioner should take into account this censored Gemora about a certain Rabbi named Yeshu -Jesus which until recently was excluded by the church (as deemed unscrupulous behaviour of their religion's founder whom was supposedly flawless) and reinstated in recent editions of tractate Sanhedrin 107b:
כדקטלינהו ינאי מלכא לרבנן אזל רבי יהושע בן פרחיה וישו לאלכסנדריא של מצרים כי הוה שלמא שלח לי' שמעון בן שטח מני ירושלים עיר הקודש ליכי אלכסנדרי' של מצרים אחותי בעלי שרוי בתוכך ואנכי יושבת שוממה קם אתא ואתרמי ליה ההוא אושפיזא עבדו ליה יקרא טובא אמר כמה יפה אכסניא זו אמר ליה רבי עיניה טרוטות אמר ליה רשע בכך אתה עוסק אפיק ארבע מאה שיפורי ושמתיה
When Yanai the King of Israel was killing all the Rabbis, Rabbi Yehoshua the son of Perachia and Yeshu his Pupil fled to Alexandria in Egypt. When there was peace again Rabbi Shimon the son of Shetach sent: "From me Yerushalayim the Holy city to you Alexandria of Egypt my sister: My husband Dwells among you and i am bereft, come back now!"
So Rabbi Yehoshua and Yeshu (after receving this coded message that it was safe to return) made his way back. On the way they came across an inn host that accorded them a lot of honour, Rabbi Yehoshua said: "What a Lovely Host!"
To which Yeshu replied: "My master did you not see? Her eyes are narrow (i.e she's ugly)."
At which point Rabbi Yehoshua was angered and retorted; "wicked man is that all you are thinking about Physical beauty?" The matter led to Yeshu being excommunicated with 400 Shofar horns.