The three optional dungeons are all tied to Side Quests, so we've listed the three of them below, the location of each dungeon, and the Side Quest they're attached to.
Eastern Temple — Eastern Hyrule Field, accessed during Let's Play a Game Side Quest
Wrecked Ship — Zora Cove, Jabul Waters, accessed during the The Zappy Shipwreck Side Quest
Hidden Ruins — Faron Wetlands, accessed during Cotton-Candy Hunt Side Quest