[tricky]

Who would do better on terrorism, R's or D's? (For exact wording, click on name of poll)
Republicans Democrats Difference (D minus R)
CNN/USA Today/Gallup 2002 57 22 -35
NBC/WSJ (RV) 2002 49 13 -36
Fox 2003 53 19 -34
ABC/WaPo (Obama v GOP) 2009 34 55 +21
Seems obvious to me the reason Republicans lost their edge is Iraq. The day Bush claimed that we invaded Iraq because they had WMDs, and tried to link Al Queda and Saddam, was the day the Republican advantage on terrorism began to disappear.
Regardless of whether you agree about why, that's quite a shift in the numbers... more than 50 points in seven years. Make a note of it. You may need it one day to correct some conventional wisdom.
Added: yes, the question of a sitting president v another party is different than generic R v D, and previous data exists on the economy for the last three presidents v congress, but not for terrorism (at least in the ABC/WaPo poll). The point remains, however, that assuming the GOP always has an edge on terrorism no matter what is out the window.

The times, they are a changin'