I have installed Java 2 Runtime Environment version 1.4.2 on 2 systems and have met the same difficulties. I can get the Mozilla plugin to work easily, also I can install J2RE and use the GUI program when viewing java programs. However the problem that plagues me is installing other programs dependent on J2RE libraries (Java was installed in the directory /usr/java/j2re1.4.2_01 all the binaries and libraries are within just as they should be). For example, if I wanted to install Lime Wire for Linux (which requires J2RE) I will get a message stating that the installer cannot find my Java Virtual Machine. I have tried placing hard links to the 'java' and 'java_vm' binaries in the /usr/java/j2re1.4.2_01/bin/ directory from the directory where I would think the java installer would search for the binary, '/usr/bin/'. Once done I have had better results, the installer will extract its installation resources and configure itself for my system's environment, however once it begins to launch the installer program itself, an error occurs. It reports that the installer cannot find libjava.so and the Java 2 Runtime Environment. I later tried to place both a sym link and a hard link of libjava.so in both /usr/lib/ and /lib/ with no success and me out of ideas, I have given up for the time being.
I know that I am probably making a common mistake for early users to Linux, any suggestions would be highly appreciated.

Something to try would be to make an entry in /etc/ld.so.conf for the location of your unfound libraries, and then invoking (as root):
ldconfig

See the ldconfig man page for details.

I have tried placing the directory /usr/java/j2re1.4.2/lib in my /etc/ld.so.conf file and executed as root ldconf with no success. Well, better said, I had success doing these things however the program installer still does not find the libjava.so file. Which seems strange because when I execute ldconf -v and view which libraries it is searching for, libjava.so exists in this list of libraries. Is it necessary to list the binary directory of java in some file too? What kind of link would be appropriate if I have to link the binaries (symbolic or hard) and does it matter which binary directory I link them to? Thank you in advance!

A lot of programs will look for the JAVA_HOME environment variable to work out where it is

Add

JAVA_HOME=complete_path_to_java_runtime_directory

export JAVA_HOME

to an appropriate file such as

/etc/profile

or your .bash_profile

logout and back in and see if it helps

if that don't work add the java /bin directory to your path but unless you're using the sdk most of the time the first way works

You also should put the /usr/java/yadayadaJRE in your PATH. You can do that either in your .bashrc or you /etc/profile. You can use a line like

PATH = $PATH:/usr/java/jre_directory
export PATH

Changing the PATH variable worked, thank you very much for your assistance!