Marlboros/Molbols or however you write it, from the Final Fantasy series, at least until FFX. Nasty bastards no matter your characters' level.

It's not an RPG, but The Butcher from Diablo 1 always sticks out for me as the ultimate boss. I think because, for starters, he was waaaaaaaaay too difficult given when you encounter him, and second, he just looked and sounded so cool! :D

LOL My first reaction was:

"99 berserkers on the wall, 99 berserkers here,
Take one out, mow him down, 98 berserkers here...."

A memorable boss was the final battle of Divinity II proper (minus the expansion). Memorable because it was the total opposite of the usual drawn-out mess...about five seconds and a few slashes, done. But getting to the battle location? Nope, that took me hours of reloads. (Seriously? In a RPG, my final mission to get to the final battle is possibly the world's worst escort quest/RTS?)

If you think he's difficult in vanilla Diablo, you obviously haven't played The Hell mod, where he has like 10,000 HP and moves as fast as your character.
But to me the most iconic thing about The Butcher is his line "Ah! Fresh meat!". Just like Bill Clinton when the White House got new female interns.

Diablo 2 has the Butcher's brother but he just didn't have the same flair. :P

Since then Slimes have become iconic for most RPGs. So they aren't truly flagship. DQ has a lot of recurring monsters - Lipsies, Gracos (recurring boss), etc.

Final Fantasy: Malboro, Tonberry. Wanted to write "Cactuar", but when I played EverQuest II , it had tons of Cactuar enemies.
Arc the Lad: Bonze.
Breath of Fire: Beak.
Disgaea: Maijin.
Phantasy Star: Fiend (name in PS II), Dark Force is flagship boss.

Some series don't have flagship monsters. Can't remember flagship monsters in Might and Magic series.

I'd have to disagree. While it's true that slime-like monsters are in a number of RPGs, I'd say that the slimes in Dragon Quest are unique all the same. So much so, that the DQ versions have appeared in nearly every DQ title to date and have even starred in a number of their own spin-off games.

Changing gears, I think that the jRPG Chrono Trigger also had a variety of unique and memorable enemies. However, for me the bulbous Nu has always remained the most unforgettable since it appears throughout the game in a variety of roles -- uncommon enemy, npc, and superboss.

I really don't see Malboro and Tonberry as iconic to Final Fantasy when neither monster appeared in that game. (Malboro first appeared in FF2 and was absent in FF3 and FF5, Tonberry first appeared in FF5, and Cactuar in FF6.) I see goblins as being more iconic, being one of the first enemies fought in the first 5 games in the series (and necessarily FF3 and FF5).

Many RPGs have monsters called Slimes, but how many have Metal Slimes?

Consider also the following strange encounters of them:

In any Dragon Quest from 1 to 7 (8 and 9 don't let enemies flee during the surprise round):
A Metal Slime draws near.
The enemy attacked before you were ready!
The Metal Slime runs away.

Or the following, most likely happening in 6 or 7 (because of the way the class system works):
A Metal Slime draws near.
[The command "RUN" is chosen.]
The party tries to run away!
But the Metal Slime blocked the escape!
The Metal Slime runs away!

Goblin is a standard monster. Monster doesn't have to appear in the very first game to become flagship monster. Goblin is also absent from FF VIII, FF X, FF VI (Chimera doesn't count) and FF XII had variation which wasn't encountered until much later in the game (FF VII Goblins are also ecnountered quite late).

Also I forgot about Chocobo.
Shining in the Darkness - Crystal Ooze.
Lufia - featured Core enemies, but principle is less or more same.
Breath of Fire had lucrative Goos (their name for Slime).
Might and Magic VII had Emerald, Sapphire and Bloodstone Oozes.
Wizardry VIII had Oozes of many, many types.
Same for Demise.
Final Fantasy had Flans of many kinds. Dark Flan (FF X) comes to mind - normal encounter on way to Lady Y., and actually much harder than most of the bosses (if you didn't bother leveling Auron). And then there is Jumbo Flan.

Though I might agree on Slimes in Dragon Quest in general for their conceptual and representative approach.

Marlboro from Final Fantasy is definitely one of the monsters that comes to mind when you think about popular monsters. Here's a video of a Marlboro from FF XV. And it shows perfectly why everyone hates them ;)

"It is pitch black. You are likely to be eaten by a grue."

Also, I can't help but think of Final Fantasy and Bahamut.

It may not have to appear to be a flagship monster for the series, but it has to appear to be a flagship monster for that game. The game "Final Fantasy" has no Marlboros, etc, so therefore they are not flagship monsters of that game.

I should also point out that Chocobos only appear as enemies in a few of the Final Fantasy games and not in any of the 2D ones.

Many wouldn't consider it a true RPG, more of some sort of JARPG, or something like that, but when I think of <span class="bold">Terranigma</span> (a game so good that makes me not care about Chrono Trigger never having been released in Europe on the SNES -- as far as I'm concerned, we got the better game out of the two), I can't help but think of Huballs. Now, Terranigma is a *huge* game with three very distinct parts, and you only encounter Huballs (purple and red variations) once, but it's the fact they're the very first enemy you get to fight in the whole game that kind of makes them memorable and you end up associating them with the game because of that.

This may be considered "cheating", since Terranigma is no D&D or classic Square JRPG, but, then again, I've always preferred ARPGs, if I can avoid turn-based combat in a game, I will, and as for the Western cRPGs, well, they always felt tedious, boring and way too complex for me. So, Terranigma it is.