For setting up computers, it really doesn't help to go too much out of the way. Like was mentioned, the Microsoft Update Catalog site is good for obtaining updates.
Then if you want to check if you've missed anything, just have a computer in-house set on automatic update to "advise but not install" so you can have an idea of what new is required. Of course, test first before you roll anything out.
The batch option that's been mentioned is definitely the easiest for update sake after install (*), especially for the situation of occasional system building as you describe. Throw them on a CD along with a batch file and you can just run the updates. There are options on "making" this batch file as well, if it gets too annoying. Then you can let Windows Update pick up the slack later if you happened to miss something on the disk.
(*) If your Windows install source is stable enough (Microsoft licenses the install key, not the source itself), you can always slipstream updates into the original source. That way you can do the install and have the updates automatically incorporated in. Again, test out of the gate to make sure you know what you have and can be confident on them before they go out the door.
I'm waiting for the white paper entitled "Finding Employment in the Era of Occupational Irrelevancy
