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?
Remove all plugins, but Essentials, and start.
Start your server without your permissions plugin.
If you're talking about the color of the messages, you can edit it in the language file. (It's inside Essentials.jar)
Try to deny/remove this permission: essentials.silentjoin.vanish
LegendChat has a Global channel, anyone can hear its messages (if they have permission); and a Local, in this one, only near people can hear (you...
Separate names with a comma.