For me, the "transformative effect" and the spiritual values are the strongest proofs.
There are people who think of the Bible like it is some magic portion, where anyone who picks it up should be transformed "by its power".
However, one cannot see the transforming power of the Bible, by the mere possession of it.
Many people possess a Bible, and hardly read it. Some don't even think that it is of much value, other than to hold it in their hand for people to see... as though it's a ticket to a ride to heaven.
You probably heard that some people open it to a random page, and place it above a baby's head.
To see the transforming power of the Bible, one has to read, study, appreciate and apply it.
Only then, would one see the transforming power, because applying its values result in a superior way of life.
This is proof for me, and it can be scientifically tested.
All that is required, is to take all the people who read, study, appreciate, and apply the principles in the Bible, along with thousands of other people, and evaluate the results.
Which of those people are less angry, less sexually immoral, less tolerant of drug or alcohol abuse, less tolerant of the use of harmful substances, like smoking cigars, getting tattooed, less tolerant of dangerous activities - car, motorcycle, snowboarding, etc., racing, less tolerant of using language that is not up-building to the hearer, less tolerant of being entertained by violence, and immorality, and exposing children to these, does not return evil to those that commit evil against them, more peaceable, etc. etc.
I am confident - guaranteed - that those who are applying - living by Bible standards, would all prove to be on one side of the chart, 100%, while on the other side there would be mixed results, none consistently having their "needle" pointing one way.
The only problem science would have in this area though, is that they cannot decide on what is immoral, and people have various opinions on morals, so for example, it may be morally acceptable to some, to "pick fairs", that is pay for sexual favors. Or, one may think it is okay to "sleep with" the neighbor's wife, because "she consents", and don't love her husband, anyway.
So the world's inconsistency, on what is morally acceptable, limits science, and so, it fails to be a good tool for measuring the proofs that exist in reality.
The other thing is, science cannot read hearts, so it is impossible to verify who really is at heart applying the scriptures. Some people are good pretenders.
So, while we have the proof, and it be really proof, science cannot verify it. Nor can atheists disprove it.