Sam is combatant number three in the disc wars, then when he's in Flynn's lightcycle, there is a 3 on the speedometer or whatever you want to call that thingh on the control console. When they step off the elevator before they get on the solar sailer, they walk across a "3"-looking symbol in the floor which Rinzler later detects they walked over. In other places too (no pun intended). Like the recognizer Sam rides in. Isn't there a transparent 3 on the floor which he looks down through to see Tron City below him? there just seem to be a lot of 3s around Sam, to the point of whoever put them there even being not quite subtle about it. This obviously means something, but what?

In western cultural parlance, this could refer to the holy trinity, but I don't see how it could allude to that here unless Sam, Quorra amd Flynn somehow represent the holy ghost, Jesus and G-d himself. I don't think that's it. You could say it refers to just the three characters in the more face-value sense, but why? It wouldn't serve much purpose to do so. Maybe it alludes to a secret and for-sure plan for the already secretly approved development of two more sequels. Come on guys, help me out here, I'm really stretching here.

I would've just assumed someone liked the number 3.... if it were me, it all would've been 12...