I keep everything.
I use Paint-Sai, and make my pages in different layers (panel outlines, skin, hair, eyes, clothes, etc., speech bubbles). Then, I do "Save As" to make the final look a .png file -- that allows me to have both a .sai version (with the separate layers), and the .png version (with all layers merged). I keep both of these just in case.
When I need to make space on my computer, I just transfer all of my pages to my portable hard drive. Got a 181 TB on that baby, hehehe