Ghetsis-- far and above the rest. He's easily the darkest final boss of the main series pokemon games, deliberately, systematically inflicting psychological abuse on the children he adopted in order to bend them to his own ends. He is like Gendo Ikari in this respect, but more evil since Ghetsis is not doing hard things for arguably the greater good. Ghetsis' motivation is entirely self-enrichment. And there is no line he will not cross. He literally tried to murder you in the sequel. Ghetsis is about as edgy as a gokemon game is going to get.
His intense battle theme with the earth-shaterring timpani just happens to be my favorite theme in the history of all pokemon. It sounds like music that the devil would dance to in the underworld. I hear tales that the G-Cis tritone is known as "The devil in music" for the dissonance it creates, which makes sense why it would be used for Ghetsis' battle theme--he is literally a devil. His name Ghetsis is also a romanization of g and c sharp if you did not know. It is not every day that your music is your name. Go Dennis go!
Team Plasma is also the best evil team because it is one that someone might actually want to join. Despite everything I said about Ghetsis being the most evil, he is also smart enough to promote a message through his organization that people would be sympathetic towards, and not sound like a plot that would result in the end of the world, at least in the original Black and White. The people who join Ghetsis in BW don't seem insane. If he was serious about Pokemon Liberation then Team Plasma would actually be the good guys in the story. They dress as knights, are led by a handsome, kind, intelligent and charismatic individual in N, and they crusade for treating pokemon not as something to capture and exploit in violent sport, but as special lifeforms that should be allowed to live in independence without being collected for the whims of human beings.
Team Plasma highlights the ambiguity of the structure in the pokemon universe we have known and loved for years, and the plea of their organization is a reasonable request. If Ghetsis stayed true to this then the player would actually be the bad guy for trying to stop Team Plasma. So it's interesting seeing this one man nearly turn the world of pokemon upside.
Last but not least, Ghetsis is really, really, extremely, super, incredibly, ridiculously, nightmarishly hard to beat in the original games. Like all the main series games you cannot turn back once you enter the Pokemon league, but in Black/White, not only do you have to beat the elite four and champion, but you have a 6th and 7th battle instead of the usual 5 since you must capture the cover legendary in between defeating the elite four and taking on the champion's whole team including *his* legendary. After all of that when you think you are through then Ghetsis pops up out of nowhere the second you defeat N without giving you any chance to save your game or reorder your team, and you must face him. Even without the surprise factor Ghetsis is a monster. His team is full of tanky Pokemon that deal massive outputs damage with high attacks and very high base power moves from stone edge to earthquakes to head charge. His team is hard to get rid of because it is bulky and really diverse with few type weaknesseses, and sometimes no weaknesseses at all like the levitating elektross. You have to slug your way through status conditions, stalls, stat drops, high critical hit ratios and a bombardment of unexpected coverage moves. The most notorious member of his team is that Hydreigon. He hits fast and like a truck, spamming max base power moves like focus blast and fire blast to Ohko yoour whole. He has perfect IVs-- which you most likely don't until post game, and no hard counters in the Unova dex. No evil team leader has put me through the sheer agony that Ghetsis did, and I don't think I have been through any in-game Pokemon battle that was this hard. For that alone he's gotta get the crown.