Anyhow, I'm running Gentoo/i386, and I use the chromium-bin ebuild in portage to keep up-to-date. Lots of things have improved, however, I still don't have the PDF plugin (Adobe) working correctly. It just opens to a dark grey screen when I click on a PDF. I see this is already reported and open, so I'm waiting on that: http://code.google.com/p/chromium/issues/detail?id=19587
My Java applets haven't been working for a while, and I seen the issue was closed involving Java + Chromium: http://code.google.com/p/chromium/issues/detail?id=16787
It has status fixed, and I never really thought to investigate until today; I just realized it says right in the bug report what needs to be done: Use libnpjp2.so (not libjavaplugin_oji.so).
I guess this is the "new" Java 2 plugin?
So, on my Gentoo machine, to fix it:
ln -s /usr/share/java-config-2/nsplugin/sun-jdk-1.6-plugin2-javaplugin.so /usr/lib/nsbrowser/plugins/javaplugin.so
Again, that worked for me, your JRE/JDK versions/paths may be different. That also may not be the most elegant way to fix it; I also assume that Gentoo will start using libnpjp2.so by default at some point. Maybe its already that way in current Gentoo? I haven't sync'd / updated in a few weeks.
I did find the "correct" Gentoo way to change the plugin: eselect java-nsplugin set sun-jdk-1.6-plugin2