Thought it was impossible?

Use these lines in your /usr/share/apache2/ssleay.cnf:

for requests:

[ req ]
req_extensions          = v3_req

[ v3_req ]
subjectAltName          = critical,DNS:site1.com,DNS:site2.net

for self signed:

[ req ]
x509_extensions         = v3_ca

[ v3_ca ]
subjectAltName          = critical,DNS:site1.com,DNS:site2.net

Then you can use apache2-ssl-certificate or openssl on that.

If you want to know more, google for subjectAltName ;)