Recently I had the same problem to include QR image/png in email. The QR image is a byte array which is generated using ZXing. We do not want to save it to a file because saving/reading from a file is too expensive (slow). So both of the answers above do not work for me. Here's what I did to solve this problem:
import javax.mail.util.ByteArrayDataSource;
import org.apache.commons.mail.ImageHtmlEmail;
...
ImageHtmlEmail email = new ImageHtmlEmail();
byte[] qrImageBytes = createQRCode(); // get your image byte array
ByteArrayDataSource qrImageDataSource = new ByteArrayDataSource(qrImageBytes, "image/png");
String contentId = email.embed(qrImageDataSource, "QR Image");
Let's say the contentId is "111122223333", then your HTML part should have this:
<img src="cid: 111122223333">
There's no need to convert the byte array to Base64 because Commons Mail does the conversion for you automatically. Hope this helps.