I'll be watching this thread too for more ideas, but I've been working on this with Soda. Basically I've gotten him to the point where he listens really well even when he is worried/scared and I feel like I have the tools in place to deal with spooks and etc when I'm riding him or on the ground.
So now I've started introducing him to scary things. Plastic bags, tarps, barrels(?), cars, apparently fallen trees are scary too (lol), and pretty much everything else. When I'm riding/leading him I watch his body language and if he is worried about something we move towards it slowly. Basically I ask him to go towards it.. he gives me a step and I release pressure, ask again-he gives-I release. If its something really scary I will approach/retreat with him (move him towards until he starts getting pretty tense, then move away, then towards again). This has been working very well so far and he is a pretty flighty horse.
During groundwork, I've been using approach/retreat with bags/sticks/rakes/tarps/pretty much everything weird. I just move it towards him until he is about ready to move away, then I back up a couple of steps... then towards him again until he's at the "breaking" point, then away again. Lots of soothing tones while this is going on. When he touches it and lets me touch him with it he gets major praise.
I don't know if this is the "right way" but its been working pretty good for me. Interested to see other responses.