As a player, I think my favorite NPCs would be a tossup between Lord Soth from Ravenloft and all the various beings who believed they were Keraptis in White Plume Mountain.
As a DM, my two favorite NPCs were Gharaleth Axom from The Speaker in Dreams and Halaster the Mad from Expedition to Undermountain. Yeah, I know, Halaster dies at the beginning of the module. Well, not Halaster exactly, but his clone. The way I tied it into Expedition to the Ruins of Greyhawk it worked really well. They way I did it was that Halaster’s clone and Iggwylv’s clone fell in love and, tired of being slaves to their masters, plotted to trap Iuz, Iggwylv and Halaster in the God Trap to drain enough of their energy to become real beings. Their attempt to trap Halaster failed because at that moment the real Iuz and Iggwylv tried to open a portal from Greyhawk to Undermountain, causing Halaster to die and triggering the start of Expedition to Undermountain module with Halaster’s Call.
I think it turned out fantastically, but you’d have to ask the players. At the end of that when they had saved Undermountain, it flowed right into Ruins of Greyhawk where they from Undermountain in Faerun to that world and then dealt with the God Trap and ended the threat to both worlds.