In my investigation so far I have found
Commons Math: http://commons.apache.org/math
JAMA (dupe I know): http://math.nist.gov/javanumerics/jama/
ojAlgo: http://ojalgo.org/
Shared scientific toolbox: http://hubris.ucsd.edu/sstj/
ojAlgo is essentially a bunch of infrastructure for linear algebra, with JAMA as one of the implementations at the back end. Commons Math is nice in that it provides some interfaces for providing operations on the various data types it provides. and Shared scientific toolbox has a lot of signal processing methods in it, as well as some parallel processing utilities. And JAMA is no longer under development (the rest still are).
Mixing and matching can be quite clumsy, so be aware.
I've mainly used ojAlgo, and the Commons Math for its statistical classes, but SST is very interesting as it really uses the language (1.5 annotation), and it's moto is prototype in Matlab, deploy in the SST. But, I've not used it seriously so I can't really endorse it.