Just off the top of my head, I'd say Sideous. I think Darth Plagueis is possibly the strongest Sith that's ever lived (excluding members of the Sith species), and after training under a guy like that, Sideous is the most serious contender for the #2 spot that I can think of. I haven't played KOTOR 2 in years though, so I don't quite remember everything about Nihilus. I actually just beat the first one last week, and I've been planning to play the second one again sometime very soon, so perhaps after I'm done with that, I'll be better prepared to make an informed decision.
I was not impressed by Nihilus. But then I was not impressed by KOTOR 2. In general I did somewhat enjoy it,but it was still disappointing with the mountains of content which should not have been cut.
Therefore I cast a vote for Sidious.
In the words of
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in his review of episode 3-
" The Emperor is just so wonderful it doesn't matter. Whether he's just filled with pure hate, or he's doing manipulative things to less smart people, or he's just being plain'o silly; the man seems to find such joy in being pure evil you gotta respect that." - "He's ****ing evil and he loves it."
Those of you who do not know Plinkett must find time to watch his reviews. They are very lulzy.