If I had a choice between an entry-level candidate with a MOOC certificate and an entry-level candidate with a Github repo with some interesting projects, I think the latter candidate would be in with a better chance.

Not all candidates are created equal however but the ones that I have hired (and ones I wish I could have hired) all had at least some sort of online coding portfolio which demonstrated a good working knowledge of data structures and algorithms.

As an engineer and an employer, I am more interested in what experience you have than your educational pedigree. I would see a MOOC certificate as neutral.