I'll add an endorsement for VueScan, an excellent tool all round.
Is your issue trying to remove a background tint, yellowed pages and so on? Setting the white balance level with a preview scan can help there.
If you're trying to reduce the size of the scanned files, then most of the common tools should have a way to convert colour to black-and-white. If you have diagrams as well then greyscale will work better and still reduce file sizes.
If your documents are text-only, and all you want is the text, how about a text recognition application? That would reduce file sizes a lot.