Manually typing "@username blah" in the entry field on a client should set in_reply_to_user, obviously. That requires a client-side change, but I think right now, the backend should help out with this; it should be done for the next few weeks at the very least.
Why be all kind about the backend assistance? Because the web UI doesn't do this right now. Until the web UI does what third-party clients are being told to, I find it hard to support any API change that breaks replies as badly as this one has.
