there are different benchmarks like

http://math.nist.gov/scimark2/
http://www.spec.org/results.html
http://kano.net/javabench/

but in general windows  is faster than linux  because of lack of security and fewer system checks.
TowerJ is known to be one of fastest JVM's on Linux
Bea JRockit is the fastest on Windows
before SUN vs MS lawsuit over MS JVM, MS JVM was also one of the fastest JVM's

Do you have any official documents about the "lack of security" and "fewer system checks" comment you made?

I should note that weblogs are not qualified as "official"!!!

You should have noted what you call official too!
Is a M$ sponsored webjunk survey official?!

I should add that the SE6's performance on Linux is as good as on windows

the guy who posted this answer is a .net programmer
his point was objection to lack of security in windows.
I don't want to waste my time arguing such a matters with this kind  of people, he is supposed to learn this stuff at his university operating system courses, if he has not I can't do any thing for him.

But about your comment

lots of <<old>> jvm  performance comparison show faster results for windows  than linux  like the ones discussed in thread:
http://lkml.org/lkml/2006/4/13/202

I think the first reasons is Sun sell Solaris not Linux, so they won't optimize their Linux JVM that much that it can beat their Solaris JVM, so as a result it may become slower than windows JVM too.

the main technical reason refers to reason described in the following quote from Sun web at the following URL:
"By comparison, on Solaris the java  threads are mapped onto user threads, which in turn are run on Lightweight processes (LWP). On Windows the threads are created inside the process itself. For this reason, creating a large number of Java threads on Solaris and Windows today is faster than on Linux. This means you might need to adjust programs that rely on platform-specific timing to take a little longer on startup when they run on Linux."

java.sun.com/.../
the problem of some JVM's performance with some Linux distros was that most linux jvms where mapping java threads into linux system process. of course system process takes much more time switching than threads or fibers.

the other technical reasons is windows (DOS) file system, windows file system becomes fragmented after a while and the file system may become corrupted you may loose your files if computer is shutdown due to power failor.

of course an operating system like BSD (and some Linux distros which come with similar file systems), which their file system avoid fragmentation and optimizes file storage and works transactional have lots of performance overhead.

some of Linux JVM performance problems can be solved with OS and JVM configurations.
now the modern +1.5 versions of JVM's from sun run as fast on linux as on windows as shown in the below link from SUN:
java.sun.com/.../5.0_performance.html

yes some Linuxes are running  Java faster than windows,
due to its open source nature Linux kernel can be tuned and trimmed of unnecessary threads to become more optimized to run Java. Redhat, Oracle and some other vendors are already providing such a distribution of Linux.

about java on SUSE as long as I know till version 8 of SLES 8 it had some big problems with java at kernel level (refer to below link from IBM)
www-128.ibm.com/.../...tualMachinePerformance.html
may be this is solved at version 9 or 10
if you are sure that Java runs on Suse as fast as windows then it should run faster on other Linux distros!

and at the end for those who like laughing at windows, you may take a look at this link:
www.webperformanceinc.com/.../index.html
specially look at the chart below "Errors per second" for windows.

Let me thank you for your comment.
Of course I was "objecting" what you said, but I also clearly understand the difference between an "objection" and an "insult".
Plus, I'm not a .net programmer, and I know that you clearly know that! But if I was, it's not like I have a disease! And I'm not sure what you meant by "this kind  of people"....

Anyway, I might have missed some concepts in my OS course, but I'm at least willing to learn.
I don't know if there's such a thing that can be reffered to as "lack of security / system checks" in windows  operating systems. If you have any resources on that, I'd be glad to be informed. From any of the members.