I used THX Optimizer and a test tone compilation CD made from NCH Test Tone Generator
http://www.nch.com.au/tonegen/index.html, and fiddled with settings for about a month. Just when I thought the settings were right, I hear the tones in the above mentioned scenes.
Try War of the Worlds at 20:49. The bystanders and cops around Tom Cruise were saying,
"You feel that?", "I feel that." "What is that, the subway?", "There's no subway here." "F-Train maybe?" "There's nothing else down there." "Well, there's someting down there, and it's moving." I was hearing some LFE, but volume was extremely low; and I was not feeling any LFE at all.
I was sure that there was something wrong with my settings because the LFE I was hearing certainly did not match the dialog at that scene.
After raising the x-over to 100 hz. and above, the missing low frequencies came to life. Now, the underground rumble of the buried machines can be both heard and felt. It was the first time that the above-quoted dialog made sense to me.
The whole trial and error process took about 3 months.
Conclusion: Test tones are insufficient. Calibration must be finalized by difficult test scenes from well-mastered DVD movies.