I found a pic of the NT06 on a vertical plane and I using a ruler I figured I could get a 120x25mm fan to JUST fit under the HSF. I'd have to make custom brackets though. But that's nothing new for me =P. 
So my setup would look like... 
PSU /w 120mm fan sucking air in and out of case
                     ^
         NT06 heatsink fins
                     ^
             120x25mm fan
                     ^
                NT06 base
Airflow would follow those arrows. I SERIOUSLY doubt I'd get any clearance between the fan and the base of the HSF. I think it should be ok though considering the fact that I the HSF base only occupies a small portion of the 120mm fan's area. 
Now... are there any issues with operating fans horizontally? I remember reading something from SPCR about fluid bearing fans being unable to operate with anything other than vertical orientations. 
Btw, what do you guys think of my plan so far?