Alfred is great for opening URLs, and it does fine with custom schemes, except for DEVONthink's.
When I try to open a URL which begins "x-devonthink-item://" Alfred doesn't recognize that it is a URL, and does a google search for the URL instead of just opening it.
I know that the x-devonthink-item scheme is registered in Launch Services, and it works everywhere else in my system (Terminal, rtf hyperlinks, etc) so I think the problem is with Alfred.