When libraries and archives scan materials, they try to do it once and do it right. If you want to scan like archivists do, select TIFF (Tagged Image File Format) and scan at at least 300 ppi (pixels per inch). If you can afford the space it takes for larger files, 600 ppi is ideal.
From this master high-resolution scan, you can generate "surrogate" files in other formats on demand. It's better for your original document to scan it once at a higher resolution, exposing it to less light.
In a few days, I'll post about an alternative format called JPEG 2000.