Iraq-Al Qaida connections are well-documented in Stephen Hayes' or Richard Miniter's books. It's obvious that Saddam and Bin laden were linked, both wanted to destroy America.
Iraq is also strongly suspected to be behind 9/11 as supportive regime. Terrorists in Salman Pack were trained to hijack planes and paid by Saddam. The Atta-Iraqi ambassador meeting in Tcheckya has been attacked by the 9/11 commission, but they had no definitive answer. It's clear now that the 9/11 commission spent more time clearing Clinton's disastrous record on the War on terrorism than looking for Saddam-Bin Laden links.
Zarkawi's group on northen Iraq was also linked with Saddam, who gave money to them. Al Qaida's operative in Afghanistan moved in Iraq in 2002.
The Al Shifa plant connection and the remarks on it by Richard Clarke are certainly interesting. The 9/11 Commission Report relegates it to a footnote though.