Judging by the image I found of the Antec 1100 case, I would suggest blowing the air INTO the case. It would appear that this would bring cool air in directly behind where the CPU is seated. This should help dissipate heat both from the motherboard and the CPU, if only slightly. I'm not sure that aiming it to blow out would pull any heat off of the motherboard (and with the motherboard acting as a barrier, it won't create a suction to pull heat out of the case... plus, you don't want to be pulling warm air over top of the motherboard). Since the fan appears to be almost flush against the board, blowing air in would at at least give you convective heat transfer (cool air would hit the board, collect heat, and then be sucked out the back or other side.).
If you do that, you might want to aim the other side to blow air out to prevent a pressure build up in the case.
Edit: Since the fan appears to be so close to the board, think about it this way: if you burned your hand and had a fan, you would have the fan blow cool air over your hand to cool it off, or would you turn the fan away from your hand to try to pull the heat off of it?
I would definitely blow cool air onto it.