As I mentioned in the post on barefoot training in the Lance STS section (of which I just read the rules and will stop posting my own opinions), when I jump in barefooted I realize that my feet exist to propel me.. It feels way better every single time. I sprint sometimes with barefeet too, although sprinting in spikes is 500 times better than nike frees, and loads my ankles more than barefoot sprints I'd say.
Jumping in shoes (maybe vibrams would work, and track spikes do), tend to reduce achilles action for me. I don't feel it there and asa result jump 2-3 inches lower