Thanks for your reply. 
In reply to your question, the POV effect is similar but not the same (I think) as the stroboscopic effect. It works because the human eye sees very high frequency pulses of light as a single continuous light. (This mechanism is used by old CRT monitors and TVs where the screen draws one line at a time)
The CD generates the POV effect.. it's primary purpose is not to generate a clock signal. However, the LEDs lighting the disk have to be turned on an off at specific times, which depend on the RPM. That's why it's important to accurately trigger interrupts.
The notch is about 1 - 2 mm (the width of a normal hack saw blade since that's what I used to cut it. 
)
Unfortunately, I don't know the exact RPM of the motor. It's a normal DVD drive motor and I'm powering it off of a 3.3V supply.
I tried using a voltage comparator (just like the one in your images.. it's an LM339) and that certainly does reduce the magnitude of the problem. (less interrupts generated) but it does still generate multiple interrupts for each passage of the notch through the detector.
How does an RC circuit work? Would that be useful here?