I use air filters, but they also lower CFM. When the filters are really dirty, my temperatures appear "up" by about 2 to 3C overall, so I know when to blow the kruft off the filters.
Since I use a pressurized imbalance between intake and outflow, the rated CFM of the fans must be higher than necessary to compensate.
I've heard many prefer no filters for the reasons I just cited, and I understand. But I don't like piles of dust accumulating in the case. I could blow it out every day (every week, every month). Since the machine is "up" 24/7, it would mean a daily or weekly ritual that I'd rather follow by observing my temperatures and cleaning up on a less frequent basis.
For my C2D "build" currently underway, my intake fans will include one or two 140mm fans at case-bottom and lower-case-front. They will ALSO include a 120mm fan positioned in the rear-center of the massive hot-swap drive cage (this is a vintage server case). I will build a duct-box around the cage, so that the draw from the fan will be spread more evenly to the vent-holes in the cage's top, bottom and sides.
There are no obstructions between the cage and case-front, since these are sliding hot-swap drive-bays. The hinged bezel-door for the case is amply vented from top to bottome of either narrow edge, and vented again at the door's very bottom. I can buy household AC duct-filter -- coarse, green-colored panels of it -- and cut them to fit the case-door vent-holes. I suspect that this type of filtering will not impair CFMs nearly as much as retail individual fan filters purchased from resellers like Frozen CPU.