(1) (println (. System getProperty \"java.library.path\"))
This gives me a list of places java looks for native extensions.
Dropping this note here since google found this post for my similar question.
The Leiningen folks have now addressed this: https://github.com/technomancy/leiningen/issues/898
If you get version 2.1.0 or later, it has the fix. See the bug for details.
UPDATE: (Aug 2013)
I have a project on github I use for experimentation with lwjgl here: https://github.com/rogerallen/hello_lwjgl
I'm also using LWJGL in my shadertone project here: https://github.com/overtone/shadertone Because Shadertone is a library, I found I needed to package up the natives myself to get it to install reasonably for projects that depend on shadertone.
If anyone has some pull with the LWJGL folks, it sure would be nice if they just put natives into appropriate subdirectories as lein expects in their clojars releases.