AFGHANISTAN
The Taliban have always been oppressive. But the Americans didn't think sop when they were negotiating a pipeline deal with them in 1998 when their representatives were welcomed to Houston, Texas. But the Taliban made a decision to award an Argentinian company the pipeline deal instead of the American UNOCAL. The same year, tow American embassies were bombed...thereafter, the Argentinian economy "mysteriously" collapsed. Taliban suddenly "became" an oppressive regime who harboured terrorists and were invaded after the WTC was downed (despite no proof being provided that Osama was behind the attacks). After they were toppled, Hamid Karzai (a former UNOCAL employee was made president) and another UNOCAL employee ws made the Afghan ambassador to the US. Thereafter, the plans for a gas pipeline were laid down and a deal was struck with the countries that supported the "war on terror" (i.e. the military dictator of Pakistan who helped the Americans).
IRAQ
Iraq has the second largest oil reserves in the world and the best quality crude oil. Their leader was becomming a thorn in the eye for the Americans and British despite being their puppet for almost two decades. They used him to invade Iran and also to suppress the Kurds and the Shi'a (this way the country was held together and a civil war was avoided - oil supplies were not to be affected). But the dictator grew a brain and started supporting the Palesitinians (a nuisance to Israelis), tried to get nuclear weapons and started questionning the puppet-master. So they had to make up an excuse to invade Iraq and take over the valuable oil fields. WMD's and "collaboration" with Al-Qaeda were the official reasons for the invasion. Although most of the world was against the invasion, the US and GB went right ahead. When they couldn't find any "WMD's", they said that the invasion was "still" justified because he was a ruthless dictator.

PALESTINE
Jews had been slaughtered in the millions in Europe and after WW2, Europe was filled with guilt! So, the British decided to give the Jews of Europe a homeland in the Middle East. This process had started decades before when The Balfour declaration was signed in 1917 and the Jews were given Palestinian territories. The Arabs united against the new country (Israel) and were later defeated (the US and GB supplied the Israelis with arsenal and much needed satelite pictures). The Israleis then captured more Palestinain land than was accorded to them by the UN and the rest is history. Now, this country has a lot to say in world politics and because of the Zionist infleunce in the USA, their foreign policy is fashionned in a way that it defends Israeli interests more than anything else.
IRAN
This is a country where the CIA led the overthrow of a democratically elected president in 1952 (Mossadeq). They installed Shah and privatised Iranian oil (read gave their oil to American/British companies). They tried to remove all traces of Islam and Persian culture by using the excuse of "modernisation", what they really were doing is westernisation. The Iranians rose up and took back their country during the Islamic Revolution. The Americans were afraid that the Revolution would have an effect in the whole of Middle East so they funded Saddam and ordered him to invade Iran. This didn't work and Iran is still owned by the Iranians, not some multi-national companies as the Americans wanted. Now, this country does NOT recognise Israel as a state and has funded Hizbollah which kicked out Israelis from Lebanon. With Iraq out of the way (for the Isralis and the oil is in American hands) the Israelis feel that there are two other countries that somehow "threaten" their existence, Iran and to a smalelr extent Syria. They have now called on their protectors the Americans to do something about it and that's why Bush has been narking on these two nations the last few years.
Theological differences you ask? maybe a few centuries ago...but the west is secular and they see Islam as a threat. The Muslim countries also sit on the most important thing that drives the American economy, OIL. two birds with one stone!