Although there are many sources for eating fish on Shabbos, are there any Torah sources which encourage one to eat fish on Yom Tov?
See Aruch Hashulchan 529:4 that one should have fish and meat on Yom Tov:
ולקבוע כל סעודה על דגים ובשר,
Mateh Ephraim 625:65/67 says similarly that one should have fish, meat, and wine:
עתה נחזור לסדר הסעודה יש לו לענג את היו"ט בדגים ובשר ושאר המטעמים ויינות משובחים כפי עשרו ויכלתו
See also Nitei Gavriel Hilchos Yom Tov Volume 2 Chapter 34 number 3 and footnote 3 there for additional sources and proofs:
There are many halachos that apply to fish, such as what beracha is recited on fish sticks, breaded fish, and gefilte fish. In addition, why do we eat fish on Shabbos and Yom Tov?