Recently, I have discovered a fancy bug affecting few version of Linux kernel. Without any warnings JVM just hangs in GC pause forever. Root cause is a improper memory access in kernel code. This post by Gil Tene gives a good technical explanation with deep emotional coloring.
While this bug is not JVM specific, there are few other multithreaded processes you can find on typical Linux box.
This recent bug make me remember few other cases there Linux screws Java badly.
Transparent huge pages
Transparent huge pages feature was introduced in 2.6.38 version of kernel. While it was intended to improve performance, a lot of people reports negative effects related to this feature, especially for memory intensive processes such as JVM and some database engines.
Leap seconds bug
Famous leap second bug in Linux has produced a whole plague across data centers in 2012. Java and MySQL were affected most badly. What a common between Java and MySQL, both are using threads extensively.
So, Linux, could you be a little more gentle with Java, please ;)