Answer: With the May 1963 issues as illustrated by Fantastic Four #14. Here's the cover to #13:
The little MC under the CCA stamp I suppose is to indicate Marvel Comics, but with the next issue, we got the look of the future:
And, not too surprisingly, they mentioned it inside the comic as well:
And as part of a "Special Announcements" section of the letters page:
Why then? Well, I suspect that May 1963 was about when Marvel could say that they had a line of superhero comics. Spiderman had gotten his own mag in March, Thor had lasted for 8 consecutive issues as the lead feature in Journey into Mystery, the Torch for 6 at Strange Tales and Iron Man and Ant-Man (temporarily) had nailed down the same roles at Tales of Suspense and Tales to Astonish. Because Marvel intended (and indeed succeeded with) doing an amazing amount of crossovers in their first several years, they needed to make sure that readers could identify their comics on a crowded shelf.
Of course, it's not as if other comics publishers hadn't noticed the value of that top-left corner before; for the entirety of the Silver Age, DC used it for their "Superman DC National Comics" seal opposite the CCA seal. And in the GA they often had pictures there of the lead feature or even a major backup:
Starman had that slot for 38 consecutive issues (most of which he was not the cover feature), while the Sandman had it for 16 issues before that. After the Superboy takeover of the lead role and the retirement of Starman and Sandman, DC hesitated for a bit, but then the top left part got labeled:
Why was that top left spot chosen? Because on a long shelf of magazines, which comics were sometimes sold on, as compared to the spinner racks, they were frequently the only thing the average kid would see as he flipped through. A familiar logo or a familiar character was a signal that it might be worth pulling the comic off the shelf and actually looking at the cover.
DC did forget about this during a good part of the Silver Age, and as Mark pointed out even when they remembered in the latter part of that era they were inconsistent and uncommitted.
