There is example how to use mime4j lib. See comments below.

package com.mozgoweb.mail.test;

import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import org.apache.james.mime4j.message.BinaryBody;
import org.apache.james.mime4j.message.BodyPart;
import org.apache.james.mime4j.message.Entity;
import org.apache.james.mime4j.message.Message;
import org.apache.james.mime4j.message.Multipart;
import org.apache.james.mime4j.message.TextBody;
import org.apache.james.mime4j.parser.Field;

/**
 *
 * @author Denis Lunev <den@mozgoweb.com>
 */

public class TestParser {

    private StringBuffer txtBody;
    private StringBuffer htmlBody;
    private ArrayList<BodyPart> attachments;

    /**
     *
     * @param fileName
     */
    public void parseMessage(String fileName) {
        FileInputStream fis = null;

        txtBody = new StringBuffer();
        htmlBody = new StringBuffer();
        attachments<BodyPart> = new ArrayList();

        try {
            //Get stream from file
            fis = new FileInputStream(fileName);
            //Create message with stream from file
            //If you want to parse String, you can use:
            //Message mimeMsg = new Message(new ByteArrayInputStream(mimeSource.getBytes()));
            Message mimeMsg = new Message(fis);

            //Get some standard headers
            System.out.println("To: " + mimeMsg.getTo().toString());
            System.out.println("From: " + mimeMsg.getFrom().toString());
            System.out.println("Subject: " + mimeMsg.getSubject());

            //Get custom header by name
            Field priorityFld = mimeMsg.getHeader().getField("X-Priority");
            //If header doesn't found it returns null
            if (priorityFld != null) {
                //Print header value
                System.out.println("Priority: " + priorityFld.getBody());
            }

            //If message contains many parts - parse all parts
            if (mimeMsg.isMultipart()) {
                Multipart multipart = (Multipart) mimeMsg.getBody();
                parseBodyParts(multipart);
            } else {
                //If it's single part message, just get text body
                String text = getTxtPart(mimeMsg);
                txtBody.append(text);
            }

            //Print text and HTML bodies
            System.out.println("Text body: " + txtBody.toString());
            System.out.println("Html body: " + htmlBody.toString());

            for (BodyPart attach : attachments) {
                String attName = attach.getFilename();
                //Create file with specified name
                FileOutputStream fos = new FileOutputStream(attName);
                try {
                    //Get attach stream, write it to file
                    BinaryBody bb = (BinaryBody) attach.getBody();
                    bb.writeTo(fos);
                } finally {
                    fos.close();
                }
            }

        } catch (IOException ex) {
            ex.fillInStackTrace();
        } finally {
            if (fis != null) {
                try {
                    fis.close();
                } catch (IOException ex) {
                    ex.printStackTrace();
                }
            }
        }
    }

    /**
     * This method classifies bodyPart as text, html or attached file
     *
     * @param multipart
     * @throws IOException
     */
    private void parseBodyParts(Multipart multipart) throws IOException {
        for (BodyPart part : multipart.getBodyParts()) {
            if (part.isMimeType("text/plain")) {
                String txt = getTxtPart(part);
                txtBody.append(txt);
            } else if (part.isMimeType("text/html")) {
                String html = getTxtPart(part);
                htmlBody.append(html);
            } else if (part.getDispositionType() != null && !part.getDispositionType().equals("")) {
                //If DispositionType is null or empty, it means that it's multipart, not attached file
                attachments.add(part);
            }

            //If current part contains other, parse it again by recursion
            if (part.isMultipart()) {
                parseBodyParts((Multipart) part.getBody());
            }
        }
    }

    /**
     *
     * @param part
     * @return
     * @throws IOException
     */
    private String getTxtPart(Entity part) throws IOException {
        //Get content from body
        TextBody tb = (TextBody) part.getBody();
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        tb.writeTo(baos);
        return new String(baos.toByteArray());
    }

    /**
     *
     * @param args
     */
    public static void main(String[] args) {

        String eml = "message.eml";

        TestParser parser = new TestParser();
        parser.parseMessage(eml);
    }
}