An answer is provided for instance in ETSI TS 101 862 "Qualified Certificate profile":
5.3 Qualified Certificate Indication
The following two techniques can be utilized to declare that a certificate is issued as a Qualified Certificate:
1) by identifying a certificate policy in the Certificate Policies extensions, as defined in clause 4.2.1.5 from
RFC 3280 [3], clearly expressing that the issuer intentionally has issued the certificate as a Qualified
Certificate and that the issuer claims compliance with annex I and annex II of the Directive [1]; or
2) by including a Qualified Certificate Statements extension with an esi4-qcStatement-1 statement as defined in
clause 5.2.1 of this profile.
Note that each Member State can interpret 1999/93/EC as they want, so the "qualified" quality of a certificate does not really mean much (for instance Diginotar used to deliver qualified certificates in the Netherlands). For some examples of qualified certificates used by the European Commission, see here