In the case of birth certificates that list a birth number and a number on the bottom left(usually next to the seal), which number should be listed as the document number on the I-9 form?

Naturally, birth certs are made at the county level.  If they're old enough, they'll differ substantially within a state and they all differ across states.

When you see more than one number (sometimes there's a number attached to the birth record and another number, like a serial number, attached to the piece of paper you are holding), it's not wrong to record both and it can be helpful if you label them.  Any auditor will be more concerned with your attempts to make the document verifiable than with your ability to get the one true number off of every BC you come across.

Edit: if you are photocopying documents submitted in fulfillment of the I-9 requirements and attaching them to the I-9, you're going to be covered anyway.  That doesn't mean you should make a habit of filling out section 2 carelessly, but it should give you peace of mind when you encounter these uncertainties.