Can't change background color of java application

Question 1

You are simply using too many static fields for no reason, which is making your class less extensible. Moreover the PictureViewer class extends JFrame and then inside it instead of using the same reference (on which you calling methods like getContentPane().add(scrollPane)) you are instead creating a new static reference by using PictureViewer viewer = new PictureViewer(), how can they both be on the same instance.

Moreover, in order to change the background of JScrollPane simply do this thingy :

scrollPane.getViewport().setBackground(Color.BLACK);

Here is your modified code, though I never went deep into it to rectify all bad practices, though I did managed to bring few of them :-)

import static javax.swing.JOptionPane.INFORMATION_MESSAGE;
import static javax.swing.JOptionPane.WARNING_MESSAGE;
import static javax.swing.JOptionPane.showMessageDialog;

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.EventQueue;
import java.awt.Dimension;
import java.awt.Graphics2D;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.image.BufferedImage;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.ObjectInput;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.concurrent.TimeUnit;

import javax.imageio.ImageIO;
import javax.swing.AbstractAction;
import javax.swing.Action;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
import javax.swing.KeyStroke;

public class PictureViewer {
    class PauseAction extends AbstractAction {
        public void actionPerformed(ActionEvent arg0) {
            pauseViewer = !pauseViewer;
        }
    }

    class QuitAction extends AbstractAction {
        public void actionPerformed(ActionEvent e) {
            stopViewer = true;
            pauseViewer = true;
            setNextToView();
            System.exit(0);
        }
    }

    static Double height;
    static final String newline = System.getProperty("line.separator");
    static boolean pauseViewer = false;
    static Dimension screensize = new Dimension();
    static boolean stopViewer = false;
    static JFrame viewer;
    static Double width;

    JLabel area = new JLabel("", JLabel.CENTER);
    int currentPic = 0;
    File dir = new File(".");
    BufferedImage image;    
    String path;
    Action pauseAction;
    int pauseTime = 5;
    Action quitAction;
    private JScrollPane scrollPane = new JScrollPane(area,  JScrollPane.VERTICAL_SCROLLBAR_NEVER,JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    ArrayList<File> thesePictures;

    private void displayGUI() {
        //Create and set up the window.
        viewer = new JFrame("Picture Viewer");
        viewer.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        viewer.setUndecorated(true);  //Remove the minimize, maximize and close buttons entirely.

        //Get the list of files to display.
        initialize();

        //Set up the content pane.
        addComponents();
        viewer.setPreferredSize(screensize);

        //Display the window.
        viewer.pack();
        viewer.setVisible(true);

        //Start showing pictures.
        while (!stopViewer) {
            try {
                showPictures();
            } catch (InterruptedException e) {
                e.printStackTrace();
            }
        }

        //Perform cleanup
        setNextToView();
    }

    public static void main(String[] args) throws IOException {
        Runnable runnable = new Runnable() {
            @Override
            public void run() {
                new PictureViewer().displayGUI();
            }
        };
        EventQueue.invokeLater(runnable);
    }

    public void addComponents() {
        //Set up actions.
        pauseAction = new PauseAction();
        quitAction = new QuitAction();
        scrollPane.getInputMap().put(KeyStroke.getKeyStroke("P"), "doPauseAction");
        scrollPane.getActionMap().put("doPauseAction", pauseAction);
        scrollPane.getInputMap().put(KeyStroke.getKeyStroke("SPACE"), "doQuitAction");
        scrollPane.getActionMap().put("doQuitAction", quitAction);
        scrollPane.getViewport().setBackground(Color.BLACK);
        viewer.add(scrollPane);
    }

    public ArrayList<File> getPictures(File dir) {
        ArrayList<File> listFiles = new ArrayList<File>(Arrays.asList(dir.listFiles()));
        int selectThis = (int) (Math.random() * listFiles.size());
        boolean emptyList = true;

        if (listFiles.get(selectThis).isDirectory()) {
            return getPictures(listFiles.get(selectThis));
        } else {
            //if the selected file is not a directory, go through the list of files and remove any directories.

            ArrayList<File> newList = new ArrayList<File>();

            for (File thisFile : listFiles) {
                if (!thisFile.isDirectory() && !thisFile.getName().contains(".next") && !thisFile.getName().contains(".jar")) {
                    newList.add(thisFile);
                }
            }

            listFiles = newList;
        }

        return listFiles;
    }

    public void initialize() {
        screensize = Toolkit.getDefaultToolkit().getScreenSize();
        height = screensize.getHeight();
        width = screensize.getWidth();
        String filePath = new File(".").getAbsolutePath();
        filePath = filePath.substring(0, filePath.length() - 1);
        String directory = "";

        while (thesePictures == null || thesePictures.size() == 0) {
            thesePictures = getPictures(dir);
        }

        String absolutePath = thesePictures.get(0).getAbsolutePath();
        path = absolutePath.substring(0,absolutePath.lastIndexOf(File.separator));

        //Look to see if the .next file exists.  If so, read in the file object.  If not, set the index to 0.
        File checkFile = new File(path + "\\.next");

        if (checkFile.exists()) {
            try {
                InputStream inputFile = new FileInputStream(path + "\\.next");
                InputStream buffer = new BufferedInputStream(inputFile);
                ObjectInput input = new ObjectInputStream(buffer);
                File lastViewedPic = (File) input.readObject();

                if (thesePictures.contains(lastViewedPic)) {
                    currentPic = thesePictures.indexOf(lastViewedPic);
                } else {
                    currentPic = 0;
                }
            } catch (FileNotFoundException e) {
                e.printStackTrace();
            } catch (IOException e) {
                e.printStackTrace();
            } catch (ClassNotFoundException e) {
                e.printStackTrace();
            } catch (Exception e) {
                e.printStackTrace();
                System.out.println("Look at " + path + "\\.next");
                System.exit(-1);
            }
        } else {
            currentPic = 0;
        }
    }

    public void readInFile(String fileName) {
        File file = new File(fileName);
        if(file.isFile()) {
            try {
                image = ImageIO.read(file);

                if (image.getWidth() > width || image.getHeight() > height) {
                    BufferedImage newImage = new BufferedImage(width.intValue(), height.intValue(), BufferedImage.TYPE_INT_RGB);
                    Graphics2D g = newImage.createGraphics();
                    g.drawImage(image, 0, 0, width.intValue(), height.intValue(), null);
                    g.dispose();
                    image = newImage;
                }
            } catch (IOException e) {
                showMessageDialog(viewer,"Does not compute !","No file read or found",INFORMATION_MESSAGE);
                e.printStackTrace();
            } catch (Exception e) {
                showMessageDialog(viewer, "Problem: " + e.getLocalizedMessage());
            }
        }
    }

    public void setImage(JLabel area){
        ImageIcon icon = new ImageIcon(image);
        area.setIcon(icon);
        viewer.repaint();
    }

    protected void setNextToView() {
        //See if the next picture to view file exists.  If not, create it.
        File checkFile = new File(path + "\\.next");

        if (!checkFile.exists()) {
            try {
                checkFile.createNewFile();
            } catch (IOException e) {
                e.printStackTrace();
            }
        }

        try {
            FileOutputStream outputFile = new FileOutputStream(path + "\\.next");
            ObjectOutputStream writer = new ObjectOutputStream(outputFile);
            writer.writeObject(thesePictures.get(currentPic));
            writer.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    private void showPictures() throws InterruptedException {
        while (!pauseViewer) {
            //If we reach the last file in the directory, switch to another directory (it could be the same directory).
            if (currentPic + 1 == thesePictures.size()) {
                currentPic = 0;
                thesePictures = new ArrayList<File>();

                while (thesePictures == null || thesePictures.size() == 0) {
                    thesePictures = getPictures(dir);
                }
            } else {
                currentPic += 1;
            }

            readInFile(thesePictures.get(currentPic).getAbsolutePath());
            setImage(area);
            TimeUnit.SECONDS.sleep(pauseTime);
        }
    }
}

Question 2

Try setting the background color of the scrollPane component. You're attaching the scroll pane to the content pane and then setting the background color of the content pane, but the scroll pane is covering the content pane so you can't see the background of the content pane.

Edit:

I've looked over your full class and found a confusing part. This is all enclosed in the PictureViewer class but you're also accessing static instances of a PictureViewer viewer;. Looking at your method again:

 public void addComponents() {
        //Set up actions.
        pauseAction = new PauseAction();
        quitAction = new QuitAction();
        scrollPane.getInputMap().put(KeyStroke.getKeyStroke("P"), "doPauseAction");
        scrollPane.getActionMap().put("doPauseAction", pauseAction);
        scrollPane.getInputMap().put(KeyStroke.getKeyStroke("SPACE"), "doQuitAction");
        scrollPane.getActionMap().put("doQuitAction", quitAction);
        scrollPane.setBackground(Color.BLACK);
        getContentPane().add(scrollPane);

        viewer.repaint();
    }

You're adding the scrollPane component to getContentPane().add(scrollPane) but the call to getContentPane() will return the content pane of the this instance and not the static viewer instance. Give this a shot:

public void addComponents() {
            //Set up actions.
            pauseAction = new PauseAction();
            quitAction = new QuitAction();
            scrollPane.getInputMap().put(KeyStroke.getKeyStroke("P"), "doPauseAction");
            scrollPane.getActionMap().put("doPauseAction", pauseAction);
            scrollPane.getInputMap().put(KeyStroke.getKeyStroke("SPACE"), "doQuitAction");
            scrollPane.getActionMap().put("doQuitAction", quitAction);
            scrollPane.setBackground(Color.BLACK);
            viewer.getContentPane().add(scrollPane);

            viewer.repaint();
        }

Question 3

The scrollpane will display the component you "focused" it on, and it will use a JViewPort as a background.

Anyway, the short story is that you have two options:

First one:

make both the scrollPane and the viewport non-opaque:

 getContentPane().setBackground(new Color(0,0,0));
 scrollPane.setOpaque(false);
 scrollPane.getViewport().setOpaque(false);

Second one:

set the background of your viewport:

 scrollPane.getViewport().setBackground(new Color(0,0,0));

Even though it's more complex, I prefer the first one, because it's conceptually more correct, in that the background of the frame is actually black. Here is the sample frame I used to try:

//imports...

public class ColoredFrame extends JFrame {

    public ColoredFrame() {
        initComponents();
    }

    private void initComponents() {
        getContentPane().setBackground(new Color(0,0,0));
        JLabel area = new JLabel("", JLabel.CENTER);
        JScrollPane scrlPane = new JScrollPane(area, JScrollPane.VERTICAL_SCROLLBAR_NEVER,JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
        scrlPane.setOpaque(false);
        scrlPane.getViewport().setOpaque(false);
        add(scrlPane);
    }

    /**
     * @param args
     */
    public static void main(String[] args) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                JFrame frm = new ColoredFrame();
                frm.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
                frm.setSize(500,500);
                frm.setVisible(true);
            }
        });

    }

}