Video game franchises are like cartoon series. At some point, there is going to be some superfluous characters you see only once. Characters who never appear again, even in very continuity-heavy series. In many video games, this curse of the appear-once-and-then-gone mostly happens to the bosses. There's just so many RPG bosses that are seen and fought only once, and then the franchise forgets about them, therefore you might forget about them too!
But despite that, the fans have a very strong memory. They can remember even the most unmemorable characters of any game, given that said game and its franchise have a dedicated fan base. As a result, no boss is truly “forgotten”; it's just that they appear once in the series and never again, which doesn't mean that it couldn't have a lasting impression on the players.
Even some final bosses suffer from this. They are often seen in a single game and then vanish from the series. Why? Nobody knows. But they weren't forgotten by the fans. For a one-time final boss to leave a lasting impression, there's a few factors: The character's involvement in the plot; its personality; the fight against it; its powers; memorable scenes; good boss music; and so on. Remember, I'm keeping the list to Nintendo series, so only bosses from Mario, Zelda, Kirby, Metroid, and other Nintendo franchises. You have every right to disagree with one or more of the entries, so if you think I didn't put in a boss you like, well, you can talk about it in the comments! Without further ado, here is my personal Top 12 one-time final Nintendo bosses!