From a posting on the user list:
I actually just found a whitepaper
"Oracle Berkeley DB Java Edition vs Apache Derby: A Performance Comparison"
http://www.oracle.com/technology/products/berkeley-db/pdf/je-derby-performance.pdf
Just copying there conclusion here:
"The Berkeley DB Java Edition Persistence API is a high performance,
complete solution for Java object persistence. Berkeley DB Java Edition
performance exceeds Derby performance in every test, by a factor of 3 to
10, clearly demonstrating the superior performance of Berkeley DB Java
Edition"
Cheers
Kasper