Definite WTF moments:
-When Sora hugs Kairi, but then goes over to Riku, and, after seeing that it really is Riku, just sits there and cries.
This almost covers the above except for the last part of it:
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-The moment when Roxas falls off of the Clock Tower.
-Mickey appearing when Sora dies in a boss battle.
-First encounter with the Nobodies as Roxas.
-The scene after a while of fighting Nobodies as Sora in TT.
-When you fight Vivi at the Struggle tournament.
-The scene that appears after you fight Axel for the first time.
-Roxas hearing DiZ's voice come from thin air.
-The scene showing Vivi badly pwning Seifer.
-Roxas suddenly blacking out.
-When Roxas sees the picture in the White Room, and after the memory, is shown bending (somewhat) with his hands on his head.
-The giant Twilight Thorn. (Pretty much only is a WTF moment the first time.)
-Sora riding on a skateboard.
-Fighting the Vivi clones.
-All scenes showing the massive number of Heartless in Radiant Garden.
-Atlantica. Musicals. 'Nuff said.
-Everyone remaining in the Organization XII always calling Sora Roxas.
-Namine being Kairi's nobody.
-One of Axel's last lines before his death. All of you should know very well what that line is.
-Xemnas not dying after about 3-4 battles.
-Almost every single f****** boss from KHI is alive again. Massive WTF moment for me.
-Axel dying. Not so much a WTF moment, but you get the point.
-Riku joining the party. He's virtually worthless. Axel would have been better...
-Axel saying, "Burn, baby!" when he (somewhat) puts the ground on fire.
-Axel's ring of fire.
-Demyx's constant using of clones.
-Demyx being very tough. Compared to OC, in Radiant Garden, he was majorly pwn-ish. Esp. on Proud.
-Demyx's switch between moods in Radiant Garden. First he says, "Aw, we do too have hearts! Don't be mad!" in an innocent sort of tune, then, after being yelled at by Donald, points to Sora and says, "Silence, traitor," in a considerably more serious and somewhat angry way.
-The world Space Paranoids. Obvious reasons.