You can continue using your system like it is (and everything seems to be working for you :-) but I would recommend two things.

First, from the example that you provided it seems that you're running LimeWire as root. It's not a good idea to use the root user anymore than you have to. If, for example, there was ever a security problem or simply a destructive bug with LimeWire or any other application that you run, you expose your system to much greater risk of compromise/damage when you use the root account. Create another user account and use that one.

Second, if you're not using Kaffe for anything else I suggest you remove it. You can remove it by becoming the root user and typing:

rpm -e kaffe

Now just make sure you've got your java bin directory (ie /usr/java/jre1.3.1-01/bin) added to your PATH environment variable in either ~/.bash_profile (your user only) or /etc/profile (all users).