Just-in-time (JIT) compilers convert part of the bytecode (as found in .class files) of a Java application to native code in order to improve execution speed. As a disadvantage, they often require more memory than simple interpreting virtual machines because both bytecode and the corresponding native code are in memory at the same time. JIT compilers are typically bundled with or a part of a virtual machine and do the conversion to native code at runtime, on demand.
The well-known Sun VMs for Windows, Linux x86 and Solaris come with the Hotspot JIT compiler. It is used by default, in order to turn it off, use the -Xint switch with the java application.
LaTTe comes with a built-in JIT compiler
This site also has a section on regular Java compilers.
http://www.complang.tuwien.ac.at/java/cacao/
JIT compiler for the Alpha platform.
http://www.trl.ibm.com/projects/jit/index_e.htm
A project for a JIT compiler, free for non-commercial use. Works with Solaris (Sparc), Linux (x86) and FreeBSD (x86). Source code is available.
A JIT compiler to be a module of the Sable VM.
A just-in-time compiler for VMs on the Intel x86 platform, works with Linux and FreeBSD. No word about the distribution model, seems to be free.