Regarding PrioQueue

So, it turns out that if I use Oracle Java in Windows instead of OpenJDK on Linux, the performance is pretty different:

 - #1 Skilgannon's Cache-hit KDTree [0.0275]
 - #2 Rednaxela's kd-tree (3rd gen) [0.0290]
 - #3 Rednaxela's kd-tree (2nd gen) [0.0309]
 - #4 Voidious' Linear search [0.5553]

The relative performance of things looks much more similar to what you saw, with a smaller difference between my 3rd and 2nd gen tree, with your one performing better.

Between OracleJava/Windows and OpenJDK/Linux, my 3rd gen tree and your cache-hit tree, swap places it seems.

java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b17)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

(Also turns out the server JVM is much better suited for the kd-tree test than the client JVM. Edited this post to switch the results to those using the server JVM)

Client JVM is not designed for heavy processing, like how the rumble is.