I have hired many who were initially rated "second place" but later upgraded.
If you are told that you were "second place" or "second choice" in the hiring process, do not despair or give up all hope. Call the company back in two to three weeks to emphasize again that you are still interested in working there. Why? For two reasons: (1) their first choice may not have worked out (the new hire may have gotten a counteroffer, a better offer, or just plain cold feet), and (2) it keeps you under consideration for any other position or future position that may come available.
The reality is that for every one hired, they may be five to ten others that were told they came in "second place." But if that is what they told you, take them on their honor and give it a shot.