Even though Stark Industries has existed in the comics since 1963, it never really had a logo. When the name did appear on a building or product (usually a building), the name has been written simply and inconsistently, like so:
This is true as recently as Avengers Vs. X-Men #1 (April 2012):
So when they made the movie Iron Man (2008), they had to create a logo for the company, and they came up with one that was simple, sleek, adaptable, and recognizable. That is to say, it's a pretty good one.
And I don't know if this is the absolute first appearance of it in comics, but it definitely appeared in this month's Ant-Man #1 (January 2015) when Scott Lang is looking for a new job.
UPDATE (6/28/16): I have found an earlier instance in Moon Knight #9 (November 2014). It's not the full logo, but it's obviously derived from it.