I find they fit in with Linux a lot better, especially if you might ever want to have more than one JDK installed, such as for testing purposes.
I have both the JRE 1_4_2_05 and JRE 1_5_0 installed and Azureus picks the 1.5.0 JRE. If I set JAVA_HOME to the 1.4.2 JRE, Azureus will not run as it is version 126.96.36.199 and requires JRE 1.5.0.
With the jpackage rpms you can also install all the good programs they offer with just a call to apt - very nice.
Now that is a definite advantage over the Sun JREs.