Depends on where the fan is I think, as well as the total fans (and their location) in the case. (see also http://www.bit-tech.net/hardware/2012/02/10/the-big-cooling-investigation/10 using Fractal Design Define R3 which has the front fan basically on top of the heatsink position rather than in front of it ... 43°C over ambient isn't that great for 1.3V however)
If the fan is centered over the heatsink (and it is mounted front to back) it probably will introduce more turbulence into the CPU cooler exhaust stream. If it is in front of the intake fan for the CPU cooler then it could be beneficial provided the flow isn't so strong that air doesn't get into the heatsink intake. The issue is if you intake air that is exhausted from the heatsink (i.e. the hot air from CPU heatsink exhaust recirculates into the top intake).
Ehume's OP states that he uses a front fan in the 5.25" bays, so it's not just top intake : there's flow pushing air into the heatsink intake.
If I'm not mistaken silverstone's FT01 has top intake.
and their video http://www.youtube.com/watch?feature=player_embedded&v=Qe-2ZqmSGug
The Silverstone Kublai KL04 also has a top intake.
Edited by AlphaC - 7/22/13 at 8:22pm