At this time, you still can't run Samba as a standalone AD domain controller. That won't happen until Samba 4.0 appears, hopefully sometime in 2010. Since Samba now has legal access to Windows networking protocols, that's only a matter of time. Samba will also be delivering support for Microsoft's SMB2. In theory, SMB2, available on Vista and later versions of Windows, delivers better network performance, but it's been troubled with security problems.
In the meantime, you can join Samba servers to an AD tree as a member server in Windows 2000 native-mode. This is a backwards compatible mode, which enables you to run run Samba 3.x, W2K (Windows 2000) server, Server 2003, and Server 2008 on the same LAN. For authentication purposes, your AD server must support LDAP (Lightweight Directory Access Protocol) and Kerberos.
Once you have Kerberos working, either MIT or Heimdal Kerberos on the Linux side, you must manually enter the Samba 3 Server information into AD. For full details on how to do that, check out Join Samba 3 to Your Active Directory Domain. With that done, your Samba's file shares and printers should then appear in the AD management consoles and to Windows clients.
Of course, you don't have to go to all that trouble. Whether you're running a SOHO (small office/home office) or a Fortune 50 company, you can just use Samba for all your file and print needs. For your basic Samba setup, simply install Samba on your Linux server. Once in place, turn it on, make sure your firewall doesn't get in the way of the SMB/CIFS protocols, and you're ready to start setting it up.
Most server-oriented Linux distributions, like Novell's openSUSE and SUSE Linux Server and Red Hat's Fedora and RHEL (Red Hat Enterprise Linux), come with GUIs (graphical user interfaces) to help you set Samba up. Use them. They'll make your life much easier.