5. DC's Millennium storyline. In an attempt to repeat the success that they had had with the original Crisis on Infinite Earths stuff, DC Comics tried to do another mega-story. This one was, to put it bluntly, an absolute dud.
4. The Legion of Super-Heroes 5 Years Later (5YL) stuff. While it was understandable that when Paul Levitz and Karen Berger left the LSH comic after writing it and editing it for at least 10 years (in the case of the former), it was a sad fact of life that whoever came in would not want to do the continuity thing. This is what we got because of it. That's not to say the 5YL period of Legion history didn't have some good moments, but really...
3. The Legion of Super-Heroes reboots, as in all of them. Every single reboot of the LSH was followed by an attempt to adjust and tweak and reconcile the reboots. This includes what Geoff Johns is doing in current "continuity" right now. While there have been some good stuff in the reboots and there has been some real doggies in there too, by and large the reboots of the LSH comics have killed the old fan base to some extent, and alienated people who started reading the reboots a couple of (re)boots ago.
2. Dr. Mayavale. One of the worst LSH foes of all-time, this villain was totally goofy and mad-as-a-hatter, and when one adds the whole business of Legionnaire past lives into it, yickkk!
1. The Legion Lost series. While it had some interesting ideas in it, having Jan Arrah (Element Lad) as a space cadet was bad enough, but making him into an evil demented god was just...heinous.
As you can see, for me, a lot of this largely stems from the Legion of Super-Heroes, but...well, never mind. So, what are your five worst comic ideas and moments?