Samba servers and multiple domains

Technically this is possible, but it's not intuitive or well-documented. Technically, you need to run multiple instances of Samba rather than using one Samba instance to control multiple domains. The Samba team is working on supplying features like this that are already implemented in Microsoft Active Directory. In your situation I have two potential solutions.

1. The way to leverage one phyical server is to run chrooted instances of Samba so you have multiple instances of Samba running on the same box but each serving your individual domains. It's not as elegant but it should work. I couldn't find a document on how to run chroot with Samba but you could use this example of best practices for chroot to give you an idea.
2. The other solution would be to check out Xen, which would allow you to run seperate Linux virtual machines with an instance of Samba in each one. The latest SUSE, 9.3, supports this, as do many other Linux distributions. This approach would require a seperate IP and host name for each installation but it would allow you to keep everything seperate from a domain perspective but consolidated on the same machine.