By default, photoshop's brush tool makes very smooth lines. This should be an almost instant give away. Scanned pencil artwork is generally too grainy unless you have a very nice scanner or draw very very dark. Even then though there will always be tale-tale signs of graininess somewhere.

"what about changing the brush type to something that looks grainy?"
It's true, you can come very close to that grainy texture by changing the default brush to something more appropriate, but alas, even with today's technology it's STILL very difficult for even the most natural looking brushes from Photoshop to look ...well natural. Pencil work is very uneven and has an almost random quality to it while a grainy photoshop brush still looks simulated.
Because of the nature of computers, it will be sometime (if not a very long time, if ever) before they reach the point of being able to replicate true natural art tools. As someone that understands computers on a lot more levels than most people, I say those afraid of technology "ruining true art" have nothing to worry about. In the end, it is just a different type of media outlet for art.

"What about image quality? Does that effect anything?"
It didn't dawn on me until recently why so many people mistook most of my black and white artwork for real scanned work until I realized I never uploaded images in their highest quality! This would result in a type of speckled "grainy" look around the edges of the lines. Another sign of scanned work.

The problem with this that when you decrease the quality of an image, even a small bit will produce unnatural speckle results.
Here is an image in an attempt to show you what I mean (note you may have to take the image into a program to zoom in if it's hard to see)
The small image is a digital, slightly reduced quality image. the larger image is a scanned drawing. They both have this grainy, speckled edge around their line art, but it's very different from each other. (take note though of the graininess that I mentioned earlier about the scanned artwork's line art)

The digital image's speckles have colors that range from being lighter then the original background image, to being just a little bit darker. Real Scanned work will generally do the opposite. The speckles will be darker then the original background image, even oftentimes having a few different hues (not shown in the image) This of course, can all vary depending on the type and quality of the scanner itself. This effects MOST scanners though.

"What about those that scan line art, then touched it up in photoshop before coloring?"
MOST (not all) will simply redo the line art digitally through tracing it on a new layer. not touch it up. Those that do touch up more than likely has special ink pens for the job.
If not that, then they use the very difficult and horribly terribly frustrating way of using what is called the "pen tool" to make Vectored line art. This is a completely different skill to normal drawing methods and is not needed nor is it advised for most artists. The only true benefit to it is having perfectly straight manipulable line art.