Ignoring my obvious stance that pretty all the RPG-exclusive bosses are underrated in terms of official usage and only focusing on relatively underrated ones within the fanbase,
O'Chunks is among the least-acknowledged SPM baddie despite being the most commonly fought. He needs more love. Likewise, Grodus from TTYD is often overlooked despite being the main antagonist for most of the game. I like his cold serious demeanor. Antasma to a lesser extent, has cool powers and an absolutely badass design, yet is often overlooked or criticized for his lack of doing much of note in his sole appearance, even though that wasn't a case of him being a bad or weak character but more of him not being used to his full potential.
Tatanga from Super Mario Land has only two appearances on a very limited game system and yet there's a lot of people who say he can't be fleshed out any more than those dated appearances. I think he and Wart both deserve another chance in a game, but of the two I think Tatanga is more underrated. He'd be a perfect character to interact with Wario or even appear in a Wario game if they don't want to use him for a Mario game. He really should up his standards for kidnapping targets though.
Koopa Kid from Mario Party recently got retconned out of a remake of a minigame he originally appeared in in favor of Bowser Jr. Koopa Kid was in GameCube Mario Parties after Bowser Jr.'s debut so I don't see what's so wrong with the party series keeping its recurring characters now vs then. They'd make good enemies in other Mario games too, and unlike other bosses it wouldn't even require changing the main antagonist as they already work for Bowser.
And pretty much all the main bosses from Paper Mario 64 were perfectly fine material for future appearances but I'm digressing into Nintendo instead of the fanbase again.