Now that I think about it, I could swear I saw an outline of someone open the door to Eugene's office during the blackout. I couldn't make out who it was, but their shape didn't look like SpongeBob's, Plankton's or Squidward's. I also don't think it was Mr. Dutchman since he would've just floated through the walls.
Oh my, I know what you must be thinking: I was the first ever culprit, so I must be the last too, right? Sorry dears, but no. That's too predictable even by Whodunnit standards. I have a very good alibi, I was near the punch bowl when the blackout happened. I think the culprit could be someone outside the box such as Bubble Bass, Sandy or Mr. Squidward.