What fraud check protocols do you all use to avoid fraud related charge backs?

In what context? The basic stuff I guess is either an agent always has eyes on and/or requirements on proof of identity, purchase etc. Note that if you do business globally there are local variations and laws to abide to.

E-commerce within the US.

OK, then I would say the above still, but within I think the first month I believe e.g. Stripe can handle it (that is the setup I have seen many times) - depending on your service level/package they would have many different fraud checks applied by default both for the initial payment and any chargebacks. Outside of a certain period of time it would require manual handling but the initial case management would be same, but with further proof needed if the initial payment can no longer be reversed. I guess different PSPs would have different options but I would strongly recommend offloading execution to the PSP whenever possible.