You can use the famous Apache Jakart library called Commons Email.
If your emails are in html format you can use this code:
HtmlEmail email = new HtmlEmail();
email.setSubject("<your subject>");
email.setHtmlMsg("<your html message body>");
email.setHostName("<host>");
email.setFrom("<from_address>");
email.addTo("<recipient_address>");
email.send();
and then attach your pdf files
EmailAttachment attachment = new EmailAttachment();
String filePath = "pathtofile";
attachment.setPath(filePath);
attachment.setDisposition(EmailAttachment.ATTACHMENT);
attachment.setDescription("description for this attachment");
email.attach(attachment);
Otherwise you should use the MultiPartEmail class.
Hope can be helpful...
ROb