Cleaning a scan basically means making the scans look good.
There are many steps in the process of cleaning a scan:
1. Colour-settings: Make sure the scan is in greyscale mode or, for colour images, RGB mode. [+] [-]
2. Rotating: Rotate the scan to have it aligned correctly. [+] [-]
3. Merging: Connecting two pages that are part of a double page spread. [+] [-]
4. Cropping: Crop out unneccessary parts of the scan. [+] [-]
Next thing is cropping out stuff that is not part of the manga.
The easiest way to crop with Photoshop is to use the rectangle selection tool (M) and draw a rectangle around everything you want to keep.
Finally you open the "image" dialogue once again and choose the option "Cut out".
If there are not white borders two opposing sides of the page, you will need to center the content, meaning you will have to move the panels to the middle of the image (V).
Notice: Pnyxtr did a cropping tool, too. Once again it is especially nice for working on batches, the readme can be read here: [link]
5. Leveling and dusting: Level the image so the blacks are black and the whites are white without damaging the greys then clean any specks that were left. [+] [-]
6. Redrawing: Complete any necessary redrawing, e.g. restoring the background behind offtexts. [+] [-]
7. Resizing: Resize your image to have a web-compatible size (depending on your group this may not be wanted) [+] [-]
8. Cleaning bubbles: Clear the text from the bubbles. [+] [-] [Action]
9. Saving: Save the image. [+] [-]
Other useful stuff pt.1: Adjustment layers. [+] [-]
Other useful stuff pt.2: Training Raws. [Low Quality]