Even though they are closely related, what you're dealing with is "AutoPlay", not "AutoRun" (distinction according to MS). Knowing that difference can make it much easier to find info when figuring out how to clean them out. :)
The AutoPlay handlers can be found in the registry at HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\AutoplayHandlers\Handlers and HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\AutoplayHandlers\EventHandlers.
To remove a handler, you should delete the associated registry key from both places. As always, make a backup first.