The image above shows how you can apply a pencil texture to your illustration in Illustrator using a Scatter Brush.
Draw & scan some samples
You start by scribbling some samples on a paper that has a rough structure, so that you get this nice texture. Then you scan the image in grayscale.
I've scanned my samples using my iPhone (6) and the Scanner Pro app. I simply take a picture, choose a setting, and save the image to my Photos. Then I sync my iPhone and grab the image from iPhoto.
Copy from Photoshop & paste into Illustrator
Next I open my file in Photoshop and select the best sample to create a Scatter Brush from and copy it. At this point I'm only guessing the sample I choose will give me the best result, but I could be wrong. So the following steps might involve a bit experimenting.
Vectorize via Image Trace
Then I go to Illustrator, create a new file, and paste the sample in my document. Next, I open the Image Trace panel (Window > Image Trace). I make sure the Preview options is checked, so I see the result, and I play around with the Threshold and Advanced settings. I also make sure the Ignore White option is selected.
Once you have a good result, you make sure to Expand the object into editable paths. Go to Object > Expand. In the window that appears make sure both Object and Fill are checked, and click OK.
Create Scatter Brush
The next thing to do is creating a Scatter Brush. Select your object and drag it into the Brush panel. By default the Scatter Brush brush type is selected. Click OK to confirm.
Enter a name in the Scatter Brush Options window that appears, and select the Tints option as Colorisation method, to make sure you can apply a color to your brush. Other settings will be set in a next step, so for now click OK.
Define the Scatter Brush options
To define the proper options for the brush, we'll first use the brush. Select the Brush tool from the Tools panel, and draw a simple line. It doesn't matter how straight or curvy this line is. Now double click the brush in the Brush panel. This will open the Scatter Brush Options window again. Make sure the Preview option is checked. Now you need to experiment a bit until you get the prefect brush stroke. First, play with the spacing. You most likely have to reduce the spacing a little so there aren't any gaps. Next, we need to break the repetition and create a bit of randomness in our brush stroke. We do this by choosing the Random option for Scatter and Rotation, and by playing with the values. If you think your brush looks fine, hit the OK button.
Apply the brush
Your brush is now ready to be applied. Select the Brush tool and paint your texture onto your illustration. In the image above I applied the brush in 2 different ways. As a highlight effect for the water, and a shadow effect for the mountains and trees. First I draw lines using the brush, I apply a proper color, then I group all the lines together, and I add a mask so the texture is only applied within the masked area. Lastly I play with the layer's Transparency mode and Opacity values. You can do this by clicking the circle icon on the right of the layer in Layers panel, and by going to the Transparency panel (Window > Transparency). I often leave the texture black but use Overlay as blend mode, and reduce the opacity. The nice thing about applying textures using a Scatter Brush is that the path you're drawing is fully editable at all times, and everything stays vector-based. So you can resize your image to any size you want. It also doesn't matter how your brush stroke lines look, and you can draw strokes on top of each other to become a more saturated result. This is a very flexible method.
There you have it! I hope it sparks some creative ideas. Think about trying other types of textures such as watercolour, paint spatters, charcoal… Have fun!