Please bear with me, as I'm new to Linux. I have Debian installed on an old ALR server with quad 200 MHz Pentium Pros. During the install process, I selected to have the necessary packages installed to use the install as a server. Now that its up and running, where do I set up the server "functions"? I would like to use this server as the "core" of a domain for a Windows network. I can talk to the windows computers over the network set up as a workgroup computer, but I want to change over to a domain system, with the Debian server as the Host. How do I do this?

For administering a server, you'll want to know how to change your startup services. It's not too difficult, you just have to know how to create symbolic links from runlevel directories (eg. /etc/rc.2) pointing to the appropriate startup script (usually in /etc/init.d). Here is a guide that will help you:
http://www.linux.com/articles/114107

Once you figure out how to do that, then you need to decide which ones to run. Since you want this to be a domain controller, you'll want to have Samba run on startup. There's full documentation at http://us1.samba.org/samba/, and I suggest you read it to learn how to further setup your server for interacting with Windows-based comptuers.

for a domain controller do "apt-get update" then "apt-get install samba". This will download SAMBA for windows network integration.

Then just change smb.conf (in /etc some where) - its got a lot of comments so you can set up a DC quite easialy.

Samba is already installed and working. I can view files on my Windows computers over the network. Now how do I make it work as a domain controller?

yeah, its well documented in the manual, you just need to mess about with smb.conf

I use samba as an NT4 replacement on my domain at home

you can look for a stepbystep manual for installing and using samba+ldap on debian on howtoforge.com

samba doesnt work well for the 2003 style networking but old-style NT4 type networking is prettymuch fully xompatible

that depends on the exact aspects of 2003 you're looking for. if you want a user directory in place you need the smb+ldap system.