I'm not that familiar with Craftbukkit's timings, but try to disable plugins that have a too high PluginEnableEvent count.
Uh, report this issue to them...
Use a more stable version.
Something is wrong with Citizens...
Are you using only "@"?
Download another version of CraftBukkit (or Spigot :))
To confirm if it's a plugin, start your server without them.
Run /timings and paste the result.
Where is the log? :)
Try to run Chunkster on your worlds.
Start your server without the folders of your worlds.
What chat plugin you have?
What if you deny/remove the permissions to join/create a faction for the default group?
You set allow-silent-join-quit as false, right? Interesting.
config.yml?
Separate names with a comma.