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It's downright silly to say that a JIT Compiled Java version of Quake is faster than a 16+ year old 32-bit, C version of Quake. (Remember Moore's Law?) If the source code is available to RECOMPILE a Java program, then it's ALSO available to recompile a C program with modern optimizations. I don't have a "side" in this debate. I only ask that the comparisons made be actual, factual, fair ones.
Cache size and speed has change. Optimizations have changed (loop unrolling can overload cache size). Numbers of CPU's/cores has changed. If we're going to compare C and Java, they should both be using--at the very least--compilers from the same era.
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