The Rules of Throwing
Throws add an extra dimension to the offensive game and are used mostly when fighting up close against your opponent. To perform a Throw, press both Front Punch and Front Kick at the same time. The controller can be in any position to perform the Throw. Forward and Down/Forward will produce a Throw that always puts the opponent onto the same side they started on. Neutral, Back, Down, or Down/Back will cause you to perform a Throw that causes you and your opponent to switch sides. You must be fairly close to the opponent to connect a Throw.
Performing a Throw outside of your throw range, however, will cause you to go into a Throw Whiff animation. During the Throw Whiff, you are completely vulnerable to any attacks. You cannot Throw opponents who are in the middle of hit stun on the ground. Also, Throws can actually be crouched under. If you hold down on the controller, your opponent's Throw will whiff regardless of how close they are to you. This leaves them very vulnerable and, typically, you will Uppercut them before they recover.
However, there is a caveat to this: you can only crouch under a Throw if you are not holding the Block button! If you Block while crouching, you CAN be thrown. So the only way to avoid the Throw is to be brave enough to crouch right in front of your opponent and not block, which means you can pretty much be hit by everything else.
Escaping a Throw
Whenever an opponent does successfully throw you, you can actually escape the Throw. Once you escape a Throw, the characters will be pushed away from each other (the distance you end up on depends on the character's Throw that was escaped). However, you must escape Front and Back Throws differently. If the opponent grabs you with a Back Throw, you can perform a Throw Escape by pressing Front Punch or Front Kick right after the opponent connects their Throw. If they perform a Front Throw, you can perform a Throw Escape by pressing either Back Punch or Back Kick right after the opponent Throws you. There are no visual cues as to which throw the opponent is performing, so it's literally a 50/50 guess if you know your opponent is going for a Throw.
However, you cannot be holding Block when trying to perform a Throw Escape. If you are thrown in the middle of blocking, you can still perform a Throw Escape... just make sure you let go of the Block button. Also, you cannot mash multiple buttons to escape both Throws. If the opponent Throws you, the game will only register the first Throw Escape attempt. So if someone grabs you with a Back Throw and quickly press Back Punch and then Front Punch in quick succession, it'll only register the Back Punch first so the Front Punch will not escape the Throw. Also, hitting both buttons at the same time will not work either.
Otherwise, you are free to perform a Throw Escape pretty much at any point. Even if you are in the delay of an attack or in a captured state, such as after Scorpion's Spear or Sub-Zero's Ice Ball, you can perform a Throw Escape if the opponent tries to throw you.
However, notice that the act of getting thrown will actually do 1% of damage right at the start no matter what. So even if you manage to perform a Throw Escape, you'll still take a very small amount of damage. So you do not escape scot-free.
Slow Throws
Throws are NOT instant in Mortal Kombat 9. You can actually start crouching after a Throw is started in time to make it whiff. So be careful with Throws, they will not get you out of a lot of sticky situations and the start up of a Throw can lose to attacks.
Air Throws
Some characters have Air Throws they can perform while Jumping that can catch opponents that are also in the air. You perform them by Jumping and, during the Jump, pressing both Front Punch and Front Kick at the same time, just like with ground Throws. Air Throws also have whiff animations if the opponent is not within range or cannot be Air Thrown. Most characters do not have Air Throws -- only a select few do. And those that have Air Throws generally have one Air Throw, so they will perform the same Air Throw no matter what direction you are holding the joystick.
Air Throws also count more as Special Attacks than Throws. You can combo into them unlike Ground Throws. Also, you can "buffer" into them from Jump Attacks like other Special Attacks that can be performed in the air. So, for example, with Smoke you can perform a Jump Kick into Air Throw against a grounded opponent and the Jump Kick will pop them into the air into your Air Throw for a combo.