The code doesn't look optimized with respect to reflection (i.e. avoiding it); maybe a lot of gc churn as well. The latter is a fact of life if you do lots of computations with lots of immutable collections, so it's important to identify parts which can be refactored to use Clojure transients and/or other mutable objects, but without "polluting" the entire program with mutable state.
Oh, good point on the reflection optimisation. That will definitely be useful for squeezing a bit more performance out of the graphics. Will be interesting to profile and see where the pain points are. From my experience the worst performance points are within Bukkit and occur when any block has gravity calculations to perform. I purposely avoided lava + water due to this.
