Two e-mail replacements that aspire toward secure communication with little actionable metadata are Bitmessage and I2pbote (runs over i2p net). Both are very much alpha, and Bitmessage has some significant work to do on how to scale up. But both are also p2p, and both automatically encrypt and decrypt all messages by default. If there are any other e-mail replacements that aspire toward security and anonymity, I'd love to hear about them.

I'm really interested in seeing one of the recently peer-reviewed secure, anonymous DHT e-mail systems (such as [1]) brought to life beyond an academic paper. I think such systems are pretty promising (i2pbote is similar).

1. http://arxiv.org/abs/1203.2668

EDIT: It occurs to me that I don't know enough about i2pbote to confidently call it "alpha" or "beta". So on retrospect, I'll just call it relatively new. But both i2pbote and bitmessage are definitely worth keeping an eye on.