Seeing that you have complete control over the hardware, I'd suggest
that you don't use either a serial connection of USB. There's an easier
way to communicate with a Java program: TCP/IP over Ethernet. Hardware
interfacing modules are available at sensible prices via electronics
outlets such as Farnell. See:

http://www.gridconnect.com/

for module descriptions and prices. IMO the benefits of using TCP/IP
rather than serial or USB are:

- the modules are sufficiently cheap that using them probably pays for
  itself in reduced development costs for the Java application. Unless,
  of course, you're developing a mass market item for a price-sensitive
  market.

- the Java application's interface to your hardware can be developed
  with the standard J2SE development kit.

- almost all PCs have a NIC these days, so a sockets based Java
  application doesn't need any communication hardware or software
  apart from the OS and the standard JRE. This makes user site
  installation much simpler.

- there is no need for extras such as RXTX or javax.comm which, in
  any case, are not particularly portable.

Disclaimer: I haven't used Xport modules to date and have no connection
with Gridconnect, but they'll my first stop if I run into the need to
interface custom hardware to a PC. For exactly the same reasons I've
previously used Parallax STAMPs rather than building custom controllers
round PIC chips.