Finding what is the most popular opening trap (in terms of games played) turns out to be quite tricky. In part his is due to the difficulty in searching for numbers, but it also depends upon what is a 'trap'. Is it the clear win of material (or mate), or is something more subtle, like a simple positional advantage?
In Muller and Knaak's "222 Opening Traps after 1.e4" they report that the "O'Kelly Trap" has been played 2,325 times in Megabase 2005. However this really is a positional trap as after 1.e4 c5 2.Nf3 a6 3.d4?! cxd4 4.Nxd4 Nf6 5.Nc3 e5 Black is thought to better as Nb5 is ruled out. However this runs perilously close to Larsen's observation that the Sicilian is a positional swindle, as White exchanges a central pawn for a wing pawn.
Even a line like 1.e4 c5 2.Nf3 e6 3.d4 cxd4 4.Nxd4 Nf6 5.Nc3 d6 6.f4 Be7?! 7.Bb5+ Bd7 8.e5 with the hope of 8 ... Nd5? 9.Nxd5 exd5 10.e6! (played 385 times) only leads to a slight advantage if Black plays correctly (ie 8. ... dxe5 etc).
Of course if you counted every game of chess ever played (not just rated/published games) I would be pretty sure that Scholars Mate would take the crown as the most popular trap ever. Indeed it may well be the case that 90% of all chess players (ok I'm guessing here) may have played at least 1 game using this trap (either setting it, or falling for it!)