Multi-Domain SSL is also known as Subject Alternate Name (SAN) and Unified Communication Certificate (UCC). As the name suggests, the prime focus of a Multi-Domain SSL is to protect several Fully Qualified Domain Names (FQDN) (which can be a top level domain or a subdomain) with a single certificate. While issuing a Multi-Domain SSL, the user has to clearly define all of the domains that they would like the certificate to cover.
Wildcard SSL allows users to obtain a certificate for a single domain. However, they can secure multiple subdomains within that primary domain. The user has to purchase the SSL certificate for the primary domain and all of the subdomains are automatically covered. For example, a wildcard SSL certificate issued for *.domain.com would protect blog.domain.com, store.domain.com, www.domain.com, etc. You would need an additional certificate to cover a second level subdomain, though, such as dev.blog.domain.com.
