konqueror and nautilus should be able to read the 64bit sun-jdk or sun-jre natively. for flash to work gnash or try out nsplugin-wrapper with the official adobe flash player.
There's still not 64-Bit Java Plug-in, i think.So if konqueror or nautilus don't have there own plugin implementation (i don't think so) then it won't run either.
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