How to avoid use of Thread.Sleep

I never gave the use of Thread.Sleep much thought, until I downloaded the latest version of Netbeans. Netbeans now warns you not to use Thread.Sleep. So I did some research on the topic and found people stating that you only need to use Thread.Sleep for debugging/testing purposes and that if you use it at any other time you have poorly written code.

So my question is how can I keep from using Thread.Sleep in the following situation.

I have written a server application that interfaces with another application. The server has two threads:

1. Handles the data coming over the socket and sends back other information or just plain acknoledgements.

2. This is the main thread. After kicking off the socket thread it going into an indefinite while loop. Within this while loop I check to make sure the socket thread is still active and that the user hasn't asked to exit the application via a TrayIcon interface. Then I sleep and continue this while loop.

With this application, the TrayIcon is the only UI.

Here is the snippet I'm referencing:

// continues running as long as the exitth file is not present and 
// the tray icon is not in a safe to exit status.

while(doNotExit())
{

    if (getPrimaryThread() == null || !getPrimaryThread().isAlive())
        resetsThreadAndSocket();

    try
    {
        // check to see if the socket threads are still active, if not create new ones.
        if ((getPrimaryThread() == null || !getPrimaryThread().isAlive()))       
            createSocketThread();

        // check right before sleeping that the user does not want to exit.
        if(getTrayIcon().isExiting())
            break;

        // puts the main Thread to sleep for 3 seconds
           Thread.sleep(3000);
    }
    catch(SQLException ex)
    {
        _log.error(ex.getMessage(), ex);
        restartDatabase();
    }
}