The Ninja is a broad-finned heatsink designed for low-airflow (and thus quiet) cooling. The Tuniq has tightly-packed fins and works best at mid-to-high airflow. The Tuniq's fan is mounted in its middle, so depending on which way round you mount it on the CPU, you only get airflow in one of two directions. It's pretty easy to mount a fan to any one of the Ninja's vertical faces, giving you four options for airflow direction.
The Ninja is a moderate-weight heatsink, about 600g without fan, and most of the weight is near the base, reducing the lever effect it exerts on an upright motherboard. The Tuniq is a big beast, nearly 800g without fan and nearly 1kg with (increased by the metal fan mounting-plate too) and it's a bit top-heavier. This has some repercussions for relative ease of installation; and certainly with a Tuniq at least, people tend to be wary about knocking their systems around too much (i.e. it won't make your pc the easiest to transport for a LAN party). Both have very solid mounting systems however, once they're in place.
When set on its lowest fanspeed (i.e. 1000rpm) the Tuniq performs about as well as the Ninja (with a typical low-airflow fan) and about as quietly.
However the tighter fins and higher surface area for heat exchange means the Tuniq gets considerably more benefit from an increase in fanspeed and airflow than the Ninja does. When the Tuniq is set to 1600rpm, it performs a good 5-7oC cooler under load than the Ninja with a 1600rpm fan attached.
The Tuniq can go as high as 2000rpm but most people at that point find the noise too intrusive. By the same logic you could mount a Delta (noisy bugger, but very high airflow) to a Ninja and get good cooling performance; but nobody wants a machine that sounds like a wind tunnel.
People tend to pick a favourite according to their own criteria. The Tuniq is a heavy, brute-force solution, but offers you scaleability and excellent cooling; while the Ninja is a quieter, lighter solution with more flexibility in airflow direction and fan choice.
And the bottom line is, both will be excellent coolers for a Core 2 Duo chip for overclocking, as C2D chips run cool at stock anyway
Hope any of that helps. I chose a Tuniq in the end, but it was a very near thing. It depends what your priorities and tastes are. Both are excellent.