cs link for prefuse source broken, so I pulled it off sourceforge :

 $ wget http://superb-east.dl.sourceforge.net/sourceforge/prefuse/
        prefuse-beta-20060411.zip

Copied sources from 
   /programming_workshop/wiki/Creating_a_simple_Graph_Visualization/
   to here, renamed with correct capitals, and fixed line endings.

On cs, java is installed in  /usr/local/jdk1.5.0_06 , so to compile prefuse
 (looking at their build.sh script)
 $ export JAVA_HOME=/usr/local/jdk1.5.0_06
 $ cd prefuse-beta
 $ chmod +x build.sh
 $ ./build.sh                (gave a list of build targets)
 $ ./build.sh prefuse        (created prefuse.jar)
 $ cp build/prefuse.jar ..   (just so it's easier to find)

Commented out "package old" in SimpleGraph.java ;
my directory structure isn't old/SimpleGraph.java .

 $ export CLASSPATH=./prefuse.jar     (... which I eventually learned is wrong)
 $ javac SimpleGraph.java
 $ java SimpleGraph

This failed with completely unhelpful error
 Exception in thread "main" java.lang.NoClassDefFoundError: SimpleGraph

Sam's jar file did work; a bit of playing around showed me that 
 (a) Sam's jar file had all of prefuse.jar, Tester.xml, and SimpleGraph.class
 (b) even after playing around with Manifest.txt files and other "jar" java stuff,
     I couldn't come up (from the command line) with a similar jar file
     that worked.  I'm sure Sam's came from Eclipse doing most of the work.
I tried several ways to get this to run, all with unhelpful errors.

Finally I saw a note in their Example.java (see below)
that says "socialnet.xml is assumed to be found at the root of the java classpath"

SO I set

 $ export CLASSPATH=.:./prefuse.jar

and then this worked :

 $ javac SimpleGraph.java       (with "package old" commented out)
 $ java SimpleGraph

------------------------------

And here's their "social network" example :

 $ wget http://prefuse.org/doc/manual/intro/socialnet.xml
 $ wget http://prefuse.org/doc/manual/intro/Example.java
 $ export CLASSPATH=.:./prefuse.jar
 $ javac Example.java
 $ java Example