Stephen F. Hayes has an interesting piece in The Weekly Standard on tracing the links between Iraq and al-Qaeda based on publicly available intelligence.
He finds that there is enough information to suggest that there were links between two, and the threat of Iraq transferring weapons of mass destruction or aiding al-Qaeda in perpetrating further terrorist attacks. There are documents in the Mukhabarat that show that Iraq sent at least one envoy to al-Qaeda in 1998, and further evidence that links Saddam Hussein to Osama bin Laden’s chief lieutenant Ayman al-Zawahiri.
Even more controversial, but not disproven, is the connection between Mohammed Atta, the ringleader of the September 11 hijackers, and an Iraqi agent in Prague:
No fewer than five high-ranking Czech officials have publicly confirmed that Mohammed Atta, the lead September 11 hijacker, met with Ahmed Khalil Ibrahim al-Ani, an Iraqi intelligence officer working at the Iraqi embassy, in Prague five months before the hijacking. Media leaks here and in the Czech Republic have called into question whether Atta was in Prague on the key dates–between April 4 and April 11, 2001. And several high-ranking administration officials are "agnostic" as to whether the meeting took place. Still, the public position of the Czech government to this day is that it did.
That assertion should be seen in the context of Atta’s curious stop-off in Prague the previous spring, as he traveled to the United States. Atta flew to Prague from Germany on May 30, 2000, but did not have a valid visa and was denied entry. He returned to Germany, obtained the proper paperwork, and took a bus back to Prague. One day later, he left for the United States.
This connection should be enough to give anyone pause. He we have a pattern of a known al-Qaeda agent travelling to Prague at least once, and leaving for the United States the next day. We also know that an-Ani was based in Prague, and many clues that the two of them may well have met.
There is a chain of evidence that suggests the real real threat of a collaboration between Iraq and al-Qaeda. Even if such a collaboration had not yet been fruitful, the fact that Iraq had attempted to work with al-Qaeda and members of al-Qaeda had been safeguarded and given aid by Iraq suggests that if anything, the evidence on this subject has been downplayed rather than exaggerated.