Here is an archive of all the past top five lists I've one over the years.
Lots of superheroes have done some shady things over the years. Cyclops of the X-Men is certainly not alone in this. But hey, it's fun to talk about, so here are the top five worst things Cyclops has ever done...
Letting the Avengers pretty much kill his son (Avengers X-Sanction #4 by Jeph Loeb and Ed McGuinness)
Cable was trying to kill the Avengers because of some weird future prophecy thing, so this one is very forgivable, especially since they didn't ACTUALLY kill him. It's still kind of weird to be all, "How do I best handle this situation? I know, I'll free the Avengers so that they can finish my crazed son off."
Having Idie kill some Hellfire Club agents (X-Men: Schism #3 by Jason Aaron and Daniel Acuna)
Idie was a new mutant (before mutants returned to the world, so she was one of only a small group of newly discovered mutants) who had grown up believing that she was a monster because of her powers. So she was pretty mentally unstable when Cyclops had her attack and kill a bunch of Hellfire Club members who had taken out a bunch of X-Men...
The problem was more that it fed into Idie's beliefs that she WAS a monster and that killing was all she was good for. At the same time, it wasn't like Cyclops PLANNED it, so I don't think it was all that big of a deal.
Betrayed Emma Frost (Avengers vs. X-Men #11 by Jonathan Hickman, Ed Brubaker, Matt Fraction, Brian Michael Bendis and Jason Aaron, Olivier Coipel and Mark Morales)
So during Avengers vs. X-Men, the Phoenix Force was returning to Earth and the X-Men and the Avengers differed over whether it was a good thing or not. Cyclops thought it was a good thing. Now, Cyclops turned out to be CORRECT, but I don't know if he necessarily had enough info to be trusted on that topic. But whatever, he was right, so I won't begrudge him too much for disagreeing with the Avengers over the Phoenix Force. So Iron Man, in an attempt to stop the Phoenix Force, ended up splitting the force up and it posssessed a few members of the X-Men, Cyclops included. The Avengers slowly defeated them one by one, but then their powers would just go to the other remaining X-Men who had the Phoenix Force. So it came down to just Cyclops and his girlfriend, Emma Frost. As the Avengers had brought in the super-powerful mind of Professor X to fight him, Cyclops decided that he needed her half of the powers, so betrayed her and took the force for himself. Now, this would be more screwed up, but again, he WAS possessed by the Phoenix Force, which we know can mess with your mind, so it is hard for me to come down too hard on him for this...