Certificate validation
There are proposals for being able to “pin” domains to a specific certificate authority (for a fee of course), in which a certificate authority is to do extra diligence before considering issuing a certificate for a “pinned” domains.
A new “pinning” header is being implemented by servers and browsers to protect against fraudulent certificates, but are not widely used yet.
Some certificate authorities use multiple clients around the world to do their domain control validation. That will not stop a local BGP hijacking of a target domain, but does stop hijacking of the certificate authority validation test traffic itself.
The Extended Validation (EV) process for certificates requires additional validation, including based on contact details provided in a qualified information source. An adversary would have to compromise that third-party source in addition to doing the BGP hijacking.
The Certificate Transparency (CT) project is working on a global repository of domains, certificates, and associated certificate authorities. CT encourages domain owners to register with a monitoring service that will notify them if another certificate is ever issued. At the moment, only EV certificates are required to be registered with CT Logs.