As there is no longer a Java6, I tried to install yed with Java7 (Oracle) or OpenJDK but both said that:
$ sh yEd-3.9_setup.sh
Unpacking JRE ...
Preparing JRE ...
yEd-3.9_setup.sh: 218: yEd-3.9_setup.sh: bin/unpack200: not found
Error unpacking jar files. The architecture or bitness (32/64)
of the bundled JVM might not match your machine.
$ java -version
java version "1.7.0_03"
Java(TM) SE Runtime Environment (build 1.7.0_03-b04)
Java HotSpot(TM) 64-Bit Server VM (build 22.1-b02, mixed mode)
$ uname -a
Linux FZ18E 3.2.0-1-amd64 #1 SMP Fri Feb 17 05:17:36 UTC 2012 x86_64 GNU/Linux