Sendfrom en senttoaddress both have [comment] and [comment-to] as arguments. Comment uses the script to put in a message, thus in a semi-standardized manner. Does comment-to encrypt the message with that public key? I'm kind of guessing in the dark without any explanation. (I'd suggest the tags API, RPC or JSON-RPC but I've no reputation)
comment and comment-to are both just stored as text with the transaction. The intent is that comment be used to store what the transaction is for, and comment-to be used to store the name of the person or organization to which you're sending the transaction.
Neither are stored anywhere besides your wallet (they're not sent with transactions), and neither are encrypted in any way.