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Here's the CPU I'm using. That was with 8GB of DDR3 running at 1066MHz, but that's intentionally underclocked by a lot. If I clock my memory up to it's rated frequency of 1600MHz the result is as follows:

 - #1 Rednaxela's kd-tree (3rd gen) [0.0276]
 - #2 Skilgannon's Cache-hit KDTree [0.0288]
 - #3 Rednaxela's kd-tree (2nd gen) [0.0340]
 - #4 Voidious' Linear search [0.5593]

A little faster all around, but not much difference with memory clock rate it seems.

The AMD Phenom II I'm using has 6MB of L3 cache, 512kB of L2 cache per-core, completely seperate.

The Intel Core i5 you're using has 3MB of L3 cache, 256kB of L2 cache per-core, though it looks like supposedly intel has some method of allowing the two cores to access eachother's L2 cache.

Java version:

java version "1.7.0_40"
OpenJDK Runtime Environment (IcedTea 2.4.1) (ArchLinux build 7.u40_2.4.1-1-x86_64)
OpenJDK 64-Bit Server VM (build 24.0-b50, mixed mode)

I have my root partition running on an SSD with the /home partition running on a spinning disk, but I doubt the disk situation affects this benchmark at all in any case.

Edit: I also find it very interesting that you get better performance numbers for the linear search, whereas I get better performance numbers for all of the trees except yours is about the same, plus the gap between my 3rd and 2nd gen tree is much larger for me than it is for you.

Edit: Since you uploaded a small update to your code this morning I tried that also. The change was small, going from 0.0288 changing to 0.0284.