I believe I've only bought two cards off Ebay and they were graded, so I guess they weren't counterfeit. Most I've acquired are from either Sportlots, Comc.com, or Beckett Marketplace so I assume they're authentic. Still others have come from trades with guys here at TCDB and again I have to assume the cards are genuine.
I doubt I'd be able to see inauthenticity in a card from a scan. The closest I've come to notice a difference is after receiving a card and it was in the card's feel. There were a couple of cards that felt much different than the rest in the set. The cards felt stiffer. They didn't have any liquid stains, nor any bubbling or surface effects that would lead me to believe it was a sort of water damage. I don't recall which specific cards they were nor if they were expensive, but in retrospect I do remember slight disappointment when I got them. Hopefully a fast one wasn't pulled on me.
"So let the children fly
And question all they see
They'll grow up wise and penetrate
The life that lives unseen"
From "When" by The Call (Written by Michael Been and Jim Goodwin)