The story...

Mohammed Atta is still alive, according to his father, as reported in newspapers like the Guardian.

Speaking from his Cairo home, Mr Atta described hearing about the attacks after returning from a holiday on the Red Sea on the evening of September 12. "My daughter called and said she was going to drop in. She stood at the door and said 'turn on the TV'," he said. Amid images of the jets crashing into the Twin Towers, he saw his son's passport photograph.

"As I saw the picture of my son," he said, "I knew that he hadn't done it. My son called me the day after the attacks on September 12 at around midday. We spoke for two minutes about this and that.
http://www.guardian.co.uk/september11/oneyearon/story/0,12361,784541,00.html

Our take...

We have a couple of problems with the account given by Attas father. Not least because it's changed since his original story. The September 2002 Guardian article mentions a phone call the day after the attacks, for example, but here's what he's reported as saying on September 19th, 2001:

his son and namesake was a shy man who could not possibly have sent a hijacked jet slicing through the first World Trade Center tower.

"Mohamed. Oh God! He is so decent, so shy and tender," said the father, a 65-year-old retired lawyer. "He was so gentle. I used to tell him, 'Toughen up, boy!'"...

The elder Atta confirmed that the picture in all the newspapers was that on his son's passport, but said the younger man might have been murdered and his documents stolen...

"I do not believe my son did it; I am sure he is alive," the father said. "He was afraid of flying."
http://www.maebrussell.com/Articles%20and%20Notes/Eqyptian%20man%20denies%20son's%20involvement%20in%20hijackings.html

This was from an interview that took place on the 18th, supposedly 6 days after the phone call from his son, yet this isn't mentioned at all. A little odd.

What’s more, an Arab News report, also published on the 19th, specifically says Atta hadn’t been in contact since the attacks:

...Atta’s father, a lawyer, said he had not heard from his son since the attack, but was confident he had nothing to do with the carnage.
http://www.arabnews.com/?page=1&section=0&article=9482&d=19&m=9&y=2001

Why not tell reporters that his son had been in touch? And if Atta really did call his father after the attacks, then what are we to make of the fathers’ reported statements after the 7/7 London bombings, which seem to tacitly accept that his son was involved?

CAIRO, Egypt (CNN) -- The father of one of the hijackers who commandeered the first plane that crashed into the World Trade Center on September 11, 2001, praised the recent terror attacks in London and said many more would follow.

Speaking to CNN producer Ayman Mohyeldin Tuesday in his apartment in the upper-middle-class Cairo suburb of Giza, Mohamed el-Amir said he would like to see more attacks like the July 7 bombings of three London subway trains and a bus that killed 52 people, plus the four bombers....

El-Amir said the attacks in the United States and the July 7 attacks in London were the beginning of what would be a 50-year religious war, in which there would be many more fighters like his son.
http://www.cnn.com/2005/WORLD/meast/07/19/atta.father.terror/indexold.html

Atta senior doesn’t appear to be the most reliable witness in this case, and certainly this one interview, apparently contradicted by other statements he’s made, falls far short of serious evidence that Atta is still alive.