JCheckBox looks bad with some themes on Ubuntu.
This issue is originally reported against NetBeans Installer (which runs on Java):
http://www.netbeans.org/issues/show_bug.cgi?id=142650

It is broken with JDK5u16 and looks much better with OpenJDK6 and jdk 6u10.
It works fine with Metal and Nimbus but looks ugly with GTK L&F.
http://www.netbeans.org/nonav/issues/showattachment.cgi/67563/ScreenShots.zip

Tony (in CC) can give more info if required.

The source code of the demo used in the issue:

package jcheckboxcheck;
import java.awt.Container;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JCheckBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;

public class Main {
    public static void main(String[] args) {
       String[] lafs = {"javax.swing.plaf.metal.MetalLookAndFeel",
            "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel",
            "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
        };
        for (String laf : lafs) {
            try {
                UIManager.getInstalledLookAndFeels();
                UIManager.setLookAndFeel(laf);
                JCheckBox box = new JCheckBox();
                JFrame theFrame = new JFrame("Label Test");
                theFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
                theFrame.setLayout(new GridBagLayout());
                Container contentPane = theFrame.getContentPane();

                contentPane.add(box, new GridBagConstraints(0,0,0,0,1,1,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(11, 11, 0, 11), 0, 0));
                theFrame.setSize(400, 100);
                theFrame.setLocation(600, 400);
                theFrame.setVisible(true);
                box.setText("This is a long, long checkbox, try it, please");
                try {
                    Thread.sleep(5000);
                } catch (InterruptedException ex) {
                    Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
                }
                theFrame.setVisible(false);
            } catch (ClassNotFoundException ex) {
            } catch (InstantiationException ex) {
            } catch (IllegalAccessException ex) {
            } catch (UnsupportedLookAndFeelException ex) {
            }
        }
        System.exit(0);
    }
}