If you purchase Kentico CMS Server License, you can install any number of completely separated Kentico CMS projects (web sites) on a single physical server. So if you have multiple customers, you will install a separate web site for each of them and all of them will be covered by a single Server License.

There's no difference whether you use 3.x or 4.x.

Regards,

Petr Palas, Kentico