The ones in the updates directory are the important ones. Those are critical to changing your system to ensure that known bugs have been fixed since the release of 4.0 awhile back. Technically, everyone running 4.0 final, should be using those updates.
The contrib sections are for contributed rpms. They are stuff that was/is being worked on and released to the public.
For example, the e-smith-email-aliases rpm that is contributed is not something that is included in the standard e-smith packaging (yet) but was contributed so that others may benefit from it. Its certainly not an update as its not something every office is going to want to use.
In the case of the e-smith-base-4.0.12-37 I think this is the rpm that is intended to work with the PPPoE contributed rpms. Contributed rpms and modules from people are not supported by e-smith (some will be in future releases) as part of the standard product, they are add-ons.
Hope that clarifies things for you.