When working with the bokken I treat it as I would any uke. That is I seek to establish a connection with it so that we may move in concert our respective motions congruent. I don't practice choreographed kata any longer, having given it up 5 years ago. I practiced the traditional bokken katas for many years and took from them what they had to offer.
Maruyama Sensei showed me there was another way to wield the bokken, a way that he showed openly but no one seemed to be able to see. It wasn't what he did; for he demonstrated the traditional movements, it was how he did it. While his students concentrated on stringing together the correct sequence of movements, he flowed like water moving through a winding, curving pipe. The strikes were there but so seamlessly were they woven into the pattern that the weapon just moved through the point of contact and continued on its way. The bokken seemed to move of its own accord as he led/followed it around.
It is from those observations that I developed my method of working with both the bokken and jo staff. The short clip below shows Simon performing some free form work with the bokken.
(Original blog post may be found here