It is known that the Vilna Gaon put 2 sectors of Chassidus in Cherem. I am wondering who has permitted them now seeing as we non-Chassidim don't make borders between them and ourselves.
According to Rav Chaim Berlin z"tl it would appear that the cherem no longer applies in what may be the earliest formal expression of the current status quo:
I heard personally from Rav Moshe Heineman, Rav of Agudath Israel Baltimore and close talmid to Rav Ahron Kotler, that one summer a student asked Rav Ahron this question. Rav Ahron answered that "the whole reason the cherem was put out against the Chassidim was because they didn't learn Gemara, but nowadays (then in the late 1950's) some of them know how to learn better than us!"
It seems to be that Rav Aharon was somewhat echoing the responsa of Rav Chaim Berlin mentioned in another answer here
להתפלל בבית הכנסת של החסידים אין שום חשש בזה, וגזירת רבינו הגר"א ז"ל לא הי' אלא בזמנו שהקילו אז בכבוד תלמידי חכמים לומדי תורה, ולא כן בימינו שהחסידים חולקים כבוד לכל לומדי תורה והם יראי ה' ושומרים תורה ומצוה
Being that the actions of the Chassidim changed, the cherem was nullified.
Note as well, that in later generations the great scions of both branches intermarried and today there is almost no hint of the past issues between Litvaks and Chassidim (aside from chabad of course). The great Rav and Posek Rav Moshe Shternbuch of the Eida Hachareidis is both a descendant of the Gr"a and the Baal Shem Tov.