Air Ride was the first thing that came to mind. It's not even that negatively viewed, most people seem to have fond memories of it, but it's honestly one of my favorite games on the console period. City Trial is just fantastic, and it's sad how poor of a job Smash Run does at recreating the fun of that mode. Air Ride, the main race mode, was also really fun. There was just a lot of content in that game in general.
DK Jungle Beat is probably the actual most underrated Gamecube game though. A platformer developed by the team behind Super Mario Galaxy with an incredibly unique and intuitive control scheme that somehow works perfectly. The best Donkey Kong platformer there is IMO, Tokyo EAD was a brilliant team from the start.
Mario Party 5 is far and away the best Mario Party game imo. A lot of people think the series stopped being good after the N64 games and I feel like those people never played 5. It pretty much has the best everything (maps, minigames, etc.), and the Battle Royale mode is like a game in itself; it's the sort of thing that would qualify as a cheap downloadable title these days.
Others....I really liked the Gamecube Pokemon RPGs back in the day. In retrospect I know they have their flaws, and they definitely don't measure up to the mainline entries, but XD in particular I think is still great on its own merits. Gauntlet: Dark Legacy and Final Fantasy: Crystal Chronicles are a blast in local MP, though the former is a multiplat and the latter requires a crazy GBA setup.