I'm almost completing an online service where people can link their domain to. Users enter domain.com that leads to webapp.com but keeps domain.com/page in the addressbar and forward that to webapp.com/page.

Currently I'm using a Alias Pointer and using the canonical tag pointing to domain.com for SEO, and this technically works fine..

But I'd like to allow for SSL, subdomains, email hosting for each domain and keep in mind that my client or I will own the domain(s). Ultimately I'd like to automate adding domain names within the webapp by my customers.

How will this affect my (customers') SEO serving hundreds of sites through 'one' webapp? is Canonical enough? More IP adresses? How much per IP?