Is it possible to detect the time difference between the moment the kernel generates an epoll and the moment the Sun JVM reads it?
i.e. time A = voltage hits the NIC; Time B = The selector from the Java NIO package is able to select the socket channel for I/O.
Solution
Use SO_TIMESTAMP and find one that actually supports timestamping and one that supports timestamps with a resolution better than milliseconds. Then you should have a chance, if you can get Java to read incoming cmsg auxiliary data.
Without good hardware support, packets will be marked by the kernel as a low-resolution unstable timer.
(Edit #1) C sample code I think 2.6.30 or newer kernel is needed:
http://www.mjmwired.net/kernel/Documentation/networking/timestamping/timestamping.c
(Edit #2) Sample code for determining kernel-to-user space latency in C:
http://vilimpoc.org/research/ku-latency/
(Edit #3) I recommend following the J-OWAMP project, which relies on high-resolution timers and packet delay testing. The OWAMP team has been plugging in Linux kernels for better SO_TIMESTAMP support.