'Until version 0.3.20, Bitcoin went into safe mode when a valid alert was received. In safe mode, all RPC commands that send BTC or get info about received BTC return an error. Current Bitcoin versions no longer go into safe mode in response to alerts.' - https://en.bitcoin.it/wiki/Alerts

Three people have the key: Theymos, Satoshi, and Gavin.

Typically it has been used to inform users of URGENT updates.