Commons Email provides only email sending functions, not parsing.
JavaMail should be fine for what you are trying to do, but it can be a little yucky in places and incredibly strict in terms of RFC compliance. You will find that email clients do not necessarily fully comply with the specification, so the problem will be handling extreme cases and oddities in terms of incoming emails.
It provides support for POP and IMAP over SSL, for more details, refer to the API:
http://java.sun.com/products/javamail/javadocs/index.html
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