But the reality is that with DEBs and a repository, RPMs, and a repository, or MSIs and a SMS or Zenworks server, things Just Work(TM).
With Java, and "Java Web Start", any regular person runs such JWS programs so infrequently, that something working the last time is little guarantee that it will work this time. They upgrade their browsers between sessions, and break Java. Upgrade Firefox from 3.0.17 to 3.5.0 and *boom* everything gets faster, except Java applets, which break. For that matter, upgrade from 3.5.1 to 3.5.2, and things break. Go to java.sun.com and spend an hour finding the right JVM, JRE, JSE, JEE, JWTF, and click through licenses 3-4 times per, and you might get the right thing to make Java work again. Or give up trying.
Java - Sun, Oracle, whatever - has shot themselves in the foot here, I grant. Their asinine redistribution policy's all but forbidding anyone else solving this really trivial problem for them. The Java technology (in the billion senses of that word) is passable.
The Java politics is so mindbogglingly stupid that it managed to drag down a pretty good hardware company to scraps a software company bought up for pennies on the dollar.
Personally, I deal with a bunch of things that run Java. The server stuff isn't that bad, it does generally Just Work (though, I'll point out that Atlassian generally encourages people to run their "bundled" apps, rather then trying to add a .war to an extant Tomcat install.... .WARs solve only self-imposed problems, but don't even bring one back to the normal of 1993, let alone making a sysadmins job easier then everything else in 2010). But the applet which was built inhouse, and the Cisco ASA tool just about never work when I try to run them after an arbitrary amount of time.
I'll grant that JWS stuff works better then getting the unbathed masses to install a fat app. Is that a really high bar to get over? Has no one at Sun looked at management tools in the last 20 years?
Comparing JWS to DEBs, RPMs, or MSIs with a reasonable and quite doable management infrastructure, Java isn't playing the same sport, let alone being in the same league.