There are several very good X-Rays in this game so I can't exactly list Top 5, each are unique for various reasons.
Kano's/Jax X-Ray - it's armored, it's a Grab with incredible reach, it has the dizzy effect because it happens when least expected.
Kitana's X-Ray - she builds meter so fast that she can throw away 3 bars for her X-Ray, it hits duck, it travels full screen, it goes through projectiles, it has armor so Kitana can use it as AA and prevent cross-ups. 31% guaranteed damage, why not use it? Kitana builds meter fast so she can afford it like the royal Princess she is.
Sonya's X-Ray - It travels very far, it guarantees 33% damage if the first hit touches you and I believe 29% if the last hit touches you. Once you let go of block during her animation, you will get X-Ray'd and there is no escape. Even if you block it, it's safe for Sonya because it puts her at an advantage. Like Kitana, Sonya builds meter very fast so this Lt. can afford it. Scaling sucks if you do a long combo so the best way to get the best damage scaling on her X-Ray is Dive Kick,2,1/4~X-Ray 44% guaranteed.
Johnny Cage's X-Ray - Parry that can get him 50% and he can land it when you least expect it.
Kung Lao's X-Ray - If you even touch him, poke him, jump at him, cross over, this X-Ray is incredible because he can combo after it. Kung Lao builds meter very, very fast so he can burn his entire meter for this.
Liu Kang's X-Ray - Armor, he can combo immediately right after he lands the X-Ray.
Sindel's X-Ray - She has armor for once LOL! The most trickiest and deceiving X-Ray in the game, it hits low.
Reptile/Jade's X-Ray - It travels through projectiles from full screen, good against zoners 35% guaranteed damage.