Actually, "Haunted" takes place in Season 3. Robin beat Slade in combat in Season 1's finale, and Slade was killed during the Season 2 Finale. Also, Robin created the Red X persona, and it was the unknown thief who impersonated Robin as a result.
A good suggestion for this list in my opinion, would be the three parter "The Alien Costume" from Spider-Man: The Animated Series.
I found "The Puppetmaster" to be a Hell of a lot more disturbing.
As disturbing as Yubel is, I'd say that Darkness, especially in the final Arc of the series; tops her.