You will likely get many different opinions on this subject.
I think alot depends on what you like to use/tend to use, or a project you might want to save up your scraps for. Personally, I use a lot of strips and small squares, so I do cut some leftovers to sizes I might have a future project in mind for. I have clear plastic bins sorted by color, except for batiks, I keep those separate. I use mostly batiks, so that bin is larger.
You can get a lot of ideas/tips from Bonnie Hunter...
www.quiltville.com