Are you perhaps testing/running GUI programs? Each time you run an
application, Eclipse launches a new java executable. If you haven't
taken care of exiting the program when the last window of your app
closes, this java executable keeps running. This would also happen if
your application runs outside an IDE.
There are several ways to close down a GUI app properly, e.g. adding an
action listener to the app's close button
   closeMyAppBtn.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
           System.exit(0);
       }
   });
or changing the default close operation of the application's frame
   JFrame myApp = createMyAppFrame();
   myApp.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

In Eclipse 3, you can use the red Terminate button of the Console View
(Window -> Show View -> Console) to end a running java executable. On
the Console View's toolbar there's also a button to switch between
consoles. Further, the Debug View in the Debug Perspective (Window ->
Open Perspective -> Other -> Debug) shows a list of launched java
applications (either running or already terminated).