Looks pretty good! One thing I noticed and would like to bring up, not sure if you have the time now, but .. to integrate with Workflow-ng, or at least to put a function in your module that updates the order status when the balance and cert amount negate each other.

I bought a product for 3.99 with a 3.99 certificate, and when I completed the order, the status was left at "Pending." It'd help if we could make that "Complete" perhaps.

Also when looking at the admin view of an order, the Total is not displaying correctly.

Subtotal: $3.99
Gift Certificates: -$3.99
Total: $3.99

Still testing but so far it looks awesome. Nice work!