Not necessarily the worst moment, but the Mario anime movie could've used a better ending. Although I'm probably just saying this as a MarioXPeach fan. Oh well, the anime movie was a LOT better than the live action thing we got, despite the ending.
I guess nowadays, the live action Mario movie could be viewed as interesting, yet grossly inaccurate (or a pile of doo-doo that should never have seen the light of day, depending on who you're asking).