Simply put, the right stick represents the weight of the player you're controlling, while the left stick represents their actual movement through space.
So if you run around with the left stick and don't touch the right, the player will just stay upright - but when you start adding movement on the right stick you get the upper body feints and so on, with the weight shifting in the direction you press on the right stick, and the eventual movement coming from the left stick. That's the obvious, basic stuff, but it goes a lot further than that.
Defending: You can use the right stick to lean in on another player when defending, e.g. muscling them off the ball, or leaning on a winger near the touchline to force him to run the ball out of play. You can use it when there's two of you in a foot race - if you think the other guy will outpace you, you can lean right into him as you go and force him away from the path of the ball (while holding square, so another defender will come in and clear up). You can use it to tackle when a foot-in tackle is not possible, by jabbing it quickly in the direction of the ball carrier, so your defender makes a sudden lurch into his path and often knocks the ball away (can concede a foul this way, though). You can use it in mid-air to stop a striker getting up for a header, e.g. if you're controlling a smaller defender stuck against a 6-foot target man as a cross comes in, you can't outjump them but you can sometimes unbalance them as they try to head it. When you're controlling a big defender - or a big centre forward or a midfield beast - the right stick is how you throw your weight around. That's what I mean by "the ugly stuff". It's the key to mastering the new physicality in PES2014.
Dribbling: Obviously the right stick is the trick stick, used in combination with the left (and R2) to pull off all the fancy stunts, but there's more to it than that. You can do all kinds of crazy shit with it - try it out on the training pitch. One of my favourite things is when you're running full pelt with a defender shoulder-to-shoulder: let go of the left stick and push the right stick in the opposite direction, and he'll do a sudden stop and turn, hopefully leaving the defender sprinting off into the middle of nowhere.
General control: You can use the right stick to trap the ball as it comes down, or to bamboozle defenders generally. When the ball is dropping towards you, flick the stick to trap it in different directions. Pushing the right stick in when you're in control of the ball flicks it up in the air, and you can also use this push-in technique (in conjunction with moving the left stick) when the ball is coming down to juggle it past defenders in a rather flashy way. Even on the ground: when you receive a pass, you can give the right stick a quick push in as you turn, to flip the ball around your marker as you sprint away.
There's more I haven't even thought of, as well - it's all very intuitive. It's the key to taking this game to the next level, as R2 was for the last few games.