See 3 posts on the subject at https://bitcointalk.org/?topic=78301.msg873713#msg873713
I'd vote to fix this by implementing per-transaction comments.
If you use a address per transaction, as recommended, they are per-address.
Per-transaction comments would be a useful addition, though we have to be careful that people don't confuse them for messages that are sent with transactions... and then being surprised that the recipient doesn't see the comment.
I think transaction-tied signed messages would be handy. Let people add them in addition to recipients, and then display the signatures out-of-band after sent (and let them view them again later by double-clicking the txn).