FF games usually have a boss to wrap up the plot neatly, but it's failed a couple times:
FF1 Chaos neatly wraps what little plot there is full circle (literally).
FF2 Emperor was fairly bland.
FF3 terrible -- no plot connection at all. Should have made Zande be the last boss.
FF4 Golbez is sweet, but Zeromus doesn't cut it for me, though he's the best of the "bad".
FF5 Exdeath well connected to the plot, but I would have liked to see Enuo.
FF6 Kefka is amazingly badass...and he's the only villain on this list to succeed with his plans.
FF7 Sephiroth is the coolest, though Kefka is still more fun.
FF8 Ultimecia doesn't get enough plot mention the first 40 hours of the game.
FF9 even worse than FF3/8 -- the endboss is a random character that hasn't been mentioned the entire game.
FFX Plotwise, the best villain yet.
As far as Nintendo goes, Ganon is the only "evil" boss that comes to mind. They've never had any other crossovers, so it's hard to say if there will be a clear boss above the bosses. Let's bring back Wart from Subspace!