Thanks sajwee,
Most of the conflicts you've mentioned are primarily political. The original cause was always some political dispute over territorial issues. Then, one bastardized form of religion or another was used to sanctify these issues and to make people feel more confident about killing not only enemy soldiers but also civilians for otherwise poor reasons. Nationalism can be used in very much the same way, but it doesn't mean it's the major cause of the war.
As for the Twin Towers attack, you know that it wasn't an attack against the entire West and that the "religious" issues involved would have had no significance had it not been for some aspects of the US foreign policy in the Middle East. This is no justification of the attack but I simply don't buy the propaganda used by many war-mongering politicians who couch the war on terrorism in religious terms thus making it totally irrational where it's not always so.