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The learning curve for OF is a bit steep, but other than that I find your description of OF's behavior a bit bizarre. OF is the least in-my-face task management application I've ever used. Did you happen to install the KranK widget? KranK intentionally pushes OF tasks at you for those who like that sort of thing. I've never seen OF launch itself, but perhaps an ill-mannered widget or Applescript is causing OF to launch on your machine. It also sounds like you installed more than one copy of OmniFocus, as that's the only way I know of to get OS X to launch two copies of the same application.

Not knowing what Dashboard widgets or scripts you've installed, it's hard to give reliable advice on uninstalling, but here goes:
  1. Launch OF, go to the Clippings tab, click the button to Remove the OmniFocus Mail Clip-o-tron 3000. If you don't have a Remove button, then the script isn't installed and you're good on this note.
  2. Open Apple Mail's preferences, go to the Rules pane, and delete any OmniFocus related rules that you might have added.
  3. Open Dashboard, click the plus sign at lower left, click the Manage Widgets button. Delete OF related widgets. There are four possible widgets that I'm aware of: OmniFidget from the OmniGroup, my Where To Focus widget, and SprialOcean's Krank and Firesprite. There may be others, but I haven't seen any yet.
  4. Now you can delete the OmniFocus application. I can't tell you how to do that because I don't know where you put it. The likely location if /Applications, but if you're getting multiple instance of OF running simultaneously, then you've probably installed it more than once.
  5. Delete the ~/Library/Application Support/OmniFocus folder.
  6. Delete ~/Library/Preferences/com.omnigroup.OmniFocus.plist file.

That should be everything. Hope that helps.