You can make the omnibox forget about URLs and search terms you've used a lot by selecting them with the down key then pressing Shift+Delete (https://superuser.com/a/189334).
Note that that doesn’t seem to work if you have a bookmark with that content (as it seems to find the bookmark, which is reasonable behavior but caught me out when I was trying to change the URL to an internal tool and didn’t realize why it wasn’t working to delete the auto-complete).