Easiest way is to use -prof, e.g:
java -prof -jar yourjar.jar
That will print a file called java.prof after the program has finished running.
See here: http://java.sun.com/developer/technicalArticles/Programming/HPROF.html
In my application I use:
-Xrunhprof:cpu=samples,thread=y,doe=y
This prints a report that contains, amongst other things, this:
CPU SAMPLES BEGIN (total = 55110) Sun Feb 7 17:02:51 2010
rank self accum count trace method
1 69.68% 69.68% 38399 300361 java.net.SocketInputStream.socketRead0
2 24.40% 94.08% 13448 300386 java.net.SocketInputStream.socketRead0
3 0.20% 94.28% 108 300425 java.io.FileOutputStream.writeBytes
4 0.19% 94.47% 107 300976 java.net.PlainDatagramSocketImpl.receive0
5 0.19% 94.65% 102 300414 package.BlockingSampleBuffer.addSample
6 0.16% 94.82% 90 300365 java.net.SocketOutputStream.socketWrite0
7 0.16% 94.98% 89 300412 package.BlockingSampleBuffer.addSample
8 0.15% 95.13% 84 300430 java.lang.Object.wait
9 0.14% 95.27% 77 300592 java.io.FileOutputStream.writeBytes
10 0.14% 95.41% 76 300566 java.lang.AbstractStringBuilder.<init>
So you can see the total time (in seconds) spent in various methods.
In mine the app spends most of its time waiting for data from a remote host (not unlikely over an internet connection).