These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: The Queen has been emotionally abusing her own daughter for Yorda's entire life, imprisoning her in a small cage hanging from a ceiling (which was actually considered a form of torture in medieval times) as well as manipulating Yorda into thinking that she'll die if she ever leaves the castle, effectively breaking her spirit. It's implied that this is the reason why Yorda is so passive during the game; it's not because she's weak, it's because she's broken. Then, there's the fact that she's been manipulating a village into sacrificing their children and that said sacrifice involves sealing those children inside of coffins until they die. And it's also implied that she controls their spirits after death as her shadow-monster servants.
Ico's character design can inspire this. If you look closely at where his bandages meet his horns, it looks like they've been torn, as if the horns sprouted abruptly. He also seems to be wearing normal children's clothes. He must've been taken away suddenly, without giving him, his family, and his friends any time to cope emotionally.
There are numerous graves throughout the castle, seeming to have been built all at the same time. They're just curiosities until you remember that they're all meant for the Queen. Just how long has she planned for her immortality and how long has she been alive?
Game Breaker: Well, as game-breaking as an item in Ico can be, but the lightsaber will clearly save you a lot of trouble, considering how tedious the shadows can be to fight with a normal weapon.
Goddamn Bats: All the shadows are this. They won't do any significant damage (except if they push you off a ledge…), but will get in your way, and you spend much time waving your stick in the air while trying to hit them.
Good Bad Bugs: In the original PAL version, setting the framerate to a certain setting allowed you to jump amazingly high with carefully-timed button presses. This made it possible to finish the game in less than an hour.
Guide Dang It: Finding the secret weapons. If you are not informed (or don't look at the trophies in the PS3 edition), you won't even suspect there are secret weapons! After all, weapons don't really have much importance to begin with and Ico isn't exactly the kind of game where you would expect such Easter eggs.
When you enter the East Arena for the first time, it will seem like you've hit a dead end. It turns out that the door to the next room is hidden in the shadows. It doesn't matter how high you turn up the brightness in-game or on your television screen. The corner of the room with the door is pitch-black. You can be stuck for hours looking for hidden switches and whacking everything with your stick.
Moral Event Horizon: At first, the Queen seems to be a worried, if arrogant mother who just wants her daughter back. But once it's revealed that she plans to kill Yorda and use her body to extend her own life...
The shadows are the souls of horned people entombed alive in the castle. Including children.
The ones in the pod room are different to those seen in the rest of the game. They're child-sized and shaped, aren't interested in you, and only want to look at the petrified Yorda. But you have to kill them, anyways.
Ico's intended fate at the beginning of the game. He's not only condemned to a tomb but also shackled. Alone and trapped in the dark, with only luck saving him from either suffocation or dehydration, whichever came first.
The walls of the tomb room are packed full of identical pods, indicating that Ico's intended fate isn't exactly unique.
Player Punch: Returning to the hall of pods where you started the game from after you're separated from Yorda — only to find her surrounded by shadows of horned boys like yourself and turned to stone. Then, killing all those shadows who mean you no harm at all.