Questions to investigate for Botany projects:

The effect of differing kinds of light upon plant growth.
The fact that plants need light to live and thrive is common knowledge. But what about the qualities of that light? Could plants fair better or worse with light that was a particular color? What about the intensity of that light? What is transpiration?

"My video teaches basic facts about plants including, what they need to survive and how they take in water. It is broken up into two main parts, facts and an experiment. The experiment demonstrates how flowers take in water by coloring a carnation." (New York, United States)

"The Effect of Lasers on Plant Growth" (Ahmed, WY, United States)

"The Effect of SPF Sunscreens in protecting against UV rays"

Questions to Investigate for Zoology Projects:

Sweat And Heat

Why does your body secrete sweat when you get hot? What is the basis for this behavior? Is the sweat almost pure water or is it salty? Why would it matter?
There are certain creatures like squid that can change their coloration to hide from predators - finding out how is a great middle school science project.