You can call the Update() method on just about any kind of collection in SharePoint, question is, when do you need to call it?
Simple answer: whenever the object has been directly modified. If you change the metadata on a column, update the column and that's it. If you change the value of a list item, update the list item, and that's it.
Update: you don't need to update a list if you've deleted an item from it or added an item to it, only if it's been changed.
Tricky one now: you add a list to a web then you add a list item to a list and then fill in the field values on that item. Update the list item, then update the list, then update the web.
Ok, it wasn't really that tricky.