Dear Rabbi, I was wondering if the minhag to overfill the cup at havdalah and spill the wine extends to motzie yom tov or only applies on motzie shabbos?

Shalom U'vracha, Great question! The minhag to overfill the havdalah cup only applies to 'motzai Shabbat', and not on 'motzai Yom Tov'. That is because on motzai Shabbat this act would be a considered a 'siman brachah' (a sign for a blessing) as it is done in the beginning of the week. On Yom Tov the minhag is not to overfill the cup (Shemirat Shabbat Kihilchata 62:7, according to the Rema 296:1). It is worth noting that the Piskei Teshuvot (296:73) does mention a minhag of the Spinka Rebbe, the author of 'Chakal Yitzhak', who did the overflowing on Yom Tov as well. However, the minhag is considered by nearly all to be only for the havdalah after Shabbat. By the way, some felt that the minhag to overfill the cup is not proper even on motzaei Shabbat because it wastes wine. Others differed and held that it's fine to 'waste' a little wine for the siman beracha (see Taz and Magen Avraham- 296) and therefore the Mishnah Berura (296:6) wrote that one should not spill too much wine, but only a small amount. All the best!