Hello!
Hmm, into the third page of a "Greatest Villain of All Time" thread on a D&D Messageboard, and no one's mentioned Lorraine Williams yet. Perhaps her image is slowly being rehabilitated...
Lots of other nice suggestions, though. Richelieu, Moriarty, the Great Old Ones, Morgoth, Dr. Doom, Vader...
Some of the more recent historical figures start to get a bit political. Hopefully no one will take it to the point of annoying the mods, especially after the recent dust-ups in other threads.
Mordred hasn't been mentioned yet. Set into motion the events leading to the destruction of Camelot.
Some of the less sane Roman Emperors might also be in the running. Nero and Caligula would seem to top that list.
Enrico Dandolo, Doge of Venice, is probably my top European pick from the Crusading period. You know his Diplomacy and Bluff Skills were maxed - he was able to divert a Christian crusading army, whose aid was badly needed in the Holy Land, from seizing the lands of their Muslim enemies to seizing the lands of his Christian neighbors, the Byzantines. What they did to the Byzantine capital, Constantinople, was the biggest looting-and-pillaging session of the entire Crusading era, and maybe of history.
The Mongols score very well in the overall body count department, though this was spread out over several generations of rulers and generals branching down from the greatest of them, Genghis Khan.
Baybars al-Bunduqdari is probably the top Middle Easterner in the running; he was the only one to beat the Mongols in open battle, and demonstrated a villainous enough streak in his treatment of Antioch and his gloating letter to its exiled ruler afterwards. His end could have come out of an gaming session, too - attempting to poison an up-and-coming young rival, getting the cups mixed up, and poisoning himself...
Machiavelli and his Borgia idols rank high in the "evil plotters and intriguers" listings.
Long John Silver is another classic Swashbuckling-adventure villain.
Dr. Doom has been mentioned, and is certainly worthy of consideration; his closest DC rivals would probably be Darkseid or
maybe Trigon when they were at their coolest. Joker was psychotic enough but somewhat small-time (at his best, about on Lecter's level), and Luthor went downhill fast when he abandoned his super-science to be a Kingpin clone.
The premiere Cold-War spy-fiction villain, Ernst Stavro Blofeld, rates at least an honorable mention (as does his parody, that mojo-stealing Springer guest and scourge of International Men of Mystery everywhere...DR. EVIL!)
The Eddoreans from the "Lensman" books probably rank up there in terms of sheer power and scale. They've certainly got the over-the-top Epic Level Psionics...

To bring about their ultimate defeat, the Arisians literally spent millions of years subtly guiding the path of evolution on planets throughout the Galaxy, employing their own vast psionic power simply to stay carefully hidden so that by the time the Eddoreans realize what is happening, it should be too late to stop the chain of events that will lead to their destruction.
And as far as D&D Villains go, I'll toss the name of the Immortal Rad into the ring. He started the rebellion that led to the cataclysmic events in Mystara known as "The Wrath of the Immortals". His followers' policy of burning all clerics at the stake was none too humanitarian, either.
So, there are a few more names to kick around. Have fun with them!
