Pencil sketches are definitely harder to scan and clean up. You can threshold the image as a way to pseudo "ink" the drawing, but I don't think it would look that great.
To be honest, I really think it's best to strive for a nice, refined, finished page. A sketch won't be able to accomplish that most of the time.
Taking the OP's comic for example, the scans to be blunt are very low quality. The images are very blurry, it looks like they haven't been leveled at all, the lighting is also inconsistent in the images so it looks more like they're photos rather than scans. If you want to do a sketch comic, then you need to take extra time to clean up the images.
When you scan, make sure the paper is flat on the scanner. Put a blank piece of paper on top of it and then put some books that are larger than the paper on top of that. The blank piece of paper will help prevent the cover of the books showing up in the scan. The books will help keep the page flat. Scan at a minimum 600dpi. This is how scanlators used to do it back in the day too. It works well. Scan in greyscale so it's faster and easier and as a TIFF file, if the option is available.
After importing to Photoshop, you'll have to bring out the rulers and line one up horizontally and the other vertically. Gosh it's been so long that I did this, but you'll have to rotate it manually, sometimes in increments of like 0.01 degrees to get it even again.
Then crop out all the space around the image that isn't part of the page.
Then level it as nostalgicroxas said. If you have a color image, you can use curves (CTRL+M) instead. It works better for color images.
Then put your text in and set the anti-aliasing to like smooth or something so it isn't pixelated.
Then save for web as a PNG. Always save the original, full size image as a PSD or TIFF.
I think that's everything.
Oh yeah, one more thing. When you scan it in, your image might be in indexed color and you won't be able to do anything with it. So just go to Image -> Mode -> Greyscale to fix it.