Bonnie Hunters Scrap User's System is great and she explains what sizes she cuts and why those specific sizes.
There's also a video of her giving a lecture at a guild and at the 5:53 mark she shows the types of units and blocks you can get out of the different scrap sizes. Worth a look, it's only a few minutes long.
Bonnie's system is very popular but it's not the be-all end-all. Some people don't like her system or the sizes she uses but in my opinion it's still worth taking a look at those two links because she does give a lot of good information that you can cherry pick to suit your own needs.
I have an old quilt magazine with an article on scraps (I'll have to go look up who wrote the article, I don't remember off hand). If you have specific block patterns in mind, she says to start keeping a few shoe boxes on hand, each one for a different quilt. For example, one box for a scrappy thousand pyramids, one for a scrappy nine patch, one for a scrappy rail fence, one for a scrappy hexagon, etc. You get the idea. Cut your scraps accordingly. And every time you're working on a new project, cut a few patches of each new fabric you're working with to feed into those scrap boxes.