I have an idea for a new verion of blender. I don’t know if it is possible to program this for Blender but if it is it sure would be a great tool.
I sometimes use a program called 3dgamestudio. This app is a block modeling game maker. Its engine has a great tool called CSG subtract. This tool is great becasue you can take any shape you want, have it touch another object, hit the CSG subtract button, and then delete the object. When you delete the object it takes along with it what ever part of the other object is was touching in its shape. So you can see how this could be a very helpful tool for cutting holes or whatever else you want out of an object.
If Blender already has a tool like this I am not aware of it. If it already has this tool please let me know how to use it.
Just a thought,