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.
Forever of the Stars: A harsh but fair alien mind who does what he must to help his people and guides the humans who really earned their freedom out of the Castle? Or a psychopathic inscrutable presence putting the characters through Hell for kicks?
In general the Forever get this treatment by parts of the fandom: A race of nigh-immortal beings who try to save humanity and themselves the best way they can, or a group of Starfish Aliens who only created humanity to farm for their emotions?
Awesome Ego: The Barbarian. A complete Jerk Ass who only cares for his own glory? You'd better believe it. Fails to learn anything from the experience and is still as unsympathetic as he started? Pretty much. But he's got an awesome voice, constantly goes on over the top Hammy speeches about the battles he's won and how glorious he is, and basically steals the scene whenever he sings.
All the emotions from the Human Equation, Agony and Fear in particular.
Fridge Brilliance: The emotions are personified and amplified into actual sentient beings rather than mere aspects of Me's personality because the program simulating Me's situation is designed for the purpose of examining raw emotion.
Growing the Beard: Into the Electric Castle is where Ayreon really took off with upped production, ambitious songwriting, fully realized Rock Opera concept and real star power in guest vocalists. It was also Ayreon's first actual commercial and critical success and regarded by many to be the Magnum Opus of the series.
The first track of the Human Equation's second disk, aptly called Trauma. It starts with 2 minutes of instrumental synths that gets you back into the story. Which then has Logic calm as ever, describe how Me's mother died of grief after Father left and never getting over the guilt. Worse still, the track gets soft and droning, until Anger gives a death metal scream, of "You're better off dead!" followed by all Me's emotions attempts of getting him to commit suicide.
The Woobie: Most protagonists and quite a few other characters qualify, but Me from the Human Equation is the most prominant..
Jerkass Woobie: Me before the resolution of Human Equation most definitely was NOT a nice person, though it is caused by much the same things that made him The Woobie in the first place.