I tend to put all of my scraps into a basket until it's over-flowing, then start cutting them up for a project. I've got one scrappy quilt pattern that I've made twice and it needed a lot of 4 patches that finish at 3". Whenever I have really small scraps, I cut those into 2" squares and put them into a zip lock bag. When that bag gets full, I turn them in to 4 patches. When my stack of 4 patches get big enough, I can make another scrappy quilt!
I hate cutting any larger pieces down without a project in mind. One of the quilt tutorials I've watched suggested cutting your scraps into strips instead of squares. That way you can decide at a later point if you need squares or rectangles for a project and cut the pieces down farther. Think of the most common sizes that you tend to use. Sort your strips by width and keep them in a labeled plastic shoebox. If you've got a bunch of 2-1/2" strips, you can cut them down into squares, rectangles, sashing, binding or whatever else you may need.