Well, this one was the winner by the most votes I’ve ever seen in a poll, so up it goes.
You’ll probably note pretty quickly that all the items on this list are psychological/emotional. Well, yes. I think scenes of physical pain, especially torture, are overused in fantasy, especially because authors have a tendency to forget about wounds whenever they would get in the way and just send their characters pelting off as if they’d never suffered. Also, psychological/emotional methods of putting people through hell mean that you get to use characters’ faults against them, and readers’ expectations for fantasy heroes against them. This is much fun.
(And if I sound like a sadist, I swear I’m not. These are simply the deepest and most affecting methods that I’ve found, which also happen to be painful).

1) Create a situation that punishes the character for using his best qualities.

Quick, what are your character’s virtues? Virtues, not flaws. You’ll think of them easily enough. A typical fantasy hero might be loyal, loving, stubborn just enough to keep going in the face of seemingly impossible odds, courageous, and defiant.
Now put that hero in a situation where he dashes into battle, trusting his soldiers to follow him, trusting the enemy to fall back before him…and have him lead all his soldiers straight into an ambush, while some of them have already betrayed him and joined the other side. His loyalty’s blinded him to needs in others (whether for greater security or more reassurance), his love and stubbornness insure he’ll stay and fight instead of pulling back, his courage has been turned into foolhardiness, and any defiance he uses to spit at and curse the enemy is energy wasted while he’s fighting for his life. And, assuming the character is also perceptive, which most of them are, he’s going to know it.
The trick here is not to make the situation seem contrived. That’s actually easier than people might think, and the easiest is probably to have an empathic enemy, a villain who understands the hero inside and out, has seen those qualities on display against him, and has ample opportunity to think up ways to counter them, having faced them on the battlefield. All that’s required is a little cleverness and a little patience to go with the empathy, and that enemy can create a trap that the hero rushes into. He’s got him coming and going.
Fantasy authors create the most extraordinary people all the time. The problem is that all those extraordinary people wind up on the hero’s side. Put one opposing the other characters—not even a true villain so much as a person with a different goal—stay true to his good qualities instead of insisting that arrogance or hatred must blind him, and the hero will willingly take enough rope to hang himself.

2) Have him mistake a present threat or enemy for one from the past.

Past evils are always showing up in fantasy. Ancient dark lords, demons who’ve slumbered through three thousand years, artifacts that once threatened the whole world and now have been found again…those are the big ones, but the theme extends even down to the idea that heroes with personal haunted pasts must face them again. Bullies show up again. Lovers scorned come back. The hero’s constant contemplation of his history becomes an asset. Fantasy readers are used to it.
Now seize that and turn it on its head.
Put the hero in front of someone or something that resembles, superficially, something or someone from his past. He may face an enemy who resembles a childhood bully, a magical threat that’s kind of like the magical threat he defeated when he was sixteen, or a romantic relationship he thinks of as a “second chance” after his first one didn’t work out. He’ll plunge in, working off prior expectations. Readers often follow right behind him. This time he’ll defeat the bully, off the magical threat even more violently, and make the love relationship work.
Except that his preconceptions have blinded him, and under the surface this threat or situation is very different, and when he meets those differences he’s going to stumble headlong.
I’m currently planning a story where one of the main characters—empathic, sensitive, brilliant in many ways—makes a strong effort to understand the other main character. She does it by relating him to someone from her past. When they clash, she reacts to him as she would that person. He promptly smashes her flat, because he’s 180 degrees different from that and she never bothered to find out.
That’s going to be one of those “victory to the darker side” sort of stories, but not all of them have to be. They can just make the hero suffer a lot.

3) Have him fail at a task he really wants to accomplish.

Not needs, wants. He may absolutely have to succeed at saving the world, or there won’t be a story and your readers will hunt you down. And given the predominance of reluctant heroes in fantasy, saving the world probably isn’t his greatest desire. I bet he was herded into it by the Wise Old Mentor and the gruff but gold-hearted warrior and the rest of the usual suspects.
No, make this something he wants. Maybe it’s to win a duel. Maybe it’s to win an art competition. Maybe it’s to finally prove to someone who thinks he’s a liar that he was right about Situation X. Maybe it’s to woo a one true love away from Obviously Stupid Rival.
Fantasy authors are very lenient good about giving these minor victories to their characters. He can even lose some far more important battles, but he’ll win these. Why? Because he wants them. And if, by some chance, he does lose, the author quickly steps in to offer the “It’s not whether you win, but how you play the game” platitude, or to point out that his love interest was stupid and simpering and not worthy of him anyway. (The last is a stupid thing for the author to do, since it hardly says flattering things about the hero’s intelligence to have him fall in love with a person like that).
So, don’t. Don’t offer the platitudes. Don’t make his rival into someone who won only because he cheated. Don’t let the hero gather the proof that his enemies somehow left lying around to show he’s not a liar. Let him fail, almost taste victory but not get it, and leave him with a stinging wound.
Maybe he’ll build bitterness around it. Maybe it’ll fester. In the name of giving fantasy heroes some damn flaws, it could work.

4) Bring his cavalier attitude down on his head.

Another common trait of a lot of fantasy heroes is to scorn another character or set of characters in the book. Not hate, the way that he might the Dark Lord, but scorn. They’re not as good as him, not as worthy of his time. They’re cowards, and therefore contemptible. They’re merchants instead of fighters or mages, and therefore contemptible. They’re his minor enemies, target practice and cannon fodder before the real thing. Quite often, this attitude extends even to the characters who do help him, but do so reluctantly.
I said in the deus ex machina rant that I would really like to see a nasty surprise overwhelm the hero at the end, where the person he depends upon to solve the problem and has treated like shit throughout the book lifts up her eyes and says, “No,” instead of “Yes.” Someone supposed to sacrifice herself so that the hero can have his blade of destiny, and all through the story he’s told her that and been self-pitying? (This from her perspective, not his). Let her refuse, and tell him why she’s refusing, and let the world go to hell because of his pride.
This does not mean that you have to make fantasy heroes so proud as to be unlikable. It means taking a step back and thinking about how other people in the story, other people who don’t have your perspective on the hero, will see him. They may be “wrong,” as you and the hero and the readers understand it. But if they are the ones slighted by his self-love, if they have reason to resent him, if there are bitternesses of their own so great in their souls that they would rather see everything fall apart than sacrifice their enmity, then bang. Let it fall apart sometimes.
And let the hero know that he could have prevented it by being a little nicer, a little more perceptive—and those are qualities that he’s supposed to have, aren’t they?

5) Inflict him with a loss he could have prevented.

It’s not the scene I hate most, it’s not the scene I despise most, but for my money the most nauseating scene in fantasy is where the hero broods about something—usually a death—that he supposedly caused, and the other character(s) in the scene reassure him that it’s not his fault. There was nothing anyone could have done, he wasn’t there, it was the other person’s faults that caused them to die, etc.
Do the nasty reversal and show that, yes, indeed, the hero could have done something. There’s a nice conduit for everlasting regret.
Once again, it doesn’t have to be deliberate. Make it the result of accident, or of the hero’s personality. If he’s suspicious of a certain lieutenant because that lieutenant has disagreed with him, and he announces, loudly, that he’s not going to give that lieutenant his protection any more…well, would it really be a surprise if someone else took the chance to kill him? A death that the bodyguards could certainly have stood in the way of? And if the hero hadn’t been such a child/paranoiac/arrogant sonofabitch, he’d still be alive.
Perhaps he knows that such-and-such a person will be a burden to the army, but he lets them come along anyway, because he’s indulgent like that. And then that person promptly gets killed or captured, in exactly the way that the hero had foreseen. Now he’s got the worry (in the case of capture) eating him alive, and the guilt eating him alive, and the regret eating him alive, and the anger of whoever was related to that person back home eating him alive. Nice.

6) Force him into a traitor’s position.

Another common fantasy trope is to force the hero to choose between two people or two ethical positions. He’s in agony, writhing, and then he chooses. Almost at once, the author reveals that the person he didn’t choose was false, or that the ethical position he didn’t choose was morally untenable anyway.
What the fuck are you doing? That’s passing up a prime opportunity for tragedy and hell, right there.
It’s perfectly possible that two friends the hero had, or two principles he holds, can coexist peacefully for a long time, and then start clashing. Duty and love are probably the two easiest principles to oppose. Yeah, sure, it might seem easy to say that a married character should give up everything for the sake of his wife, but when he’s also the leader of a city-state and thousands of other lives hang in the balance? Is it really that easy?
Well, yes, usually, it is, because the author sends an army to save the city, or makes the wife a traitor. Don’t. Make the character choose, and live with his choice, and burn with it, and die with it if need be. People will look at him as a traitor. He might look at himself as a traitor (although I presume he still has his reasons for making the decision). So be it.

7) Have him kill the thing he loves.

Oscar Wilde said it best, in “The Ballad of Reading Gaol”:

And all men kill the thing they love,
By all let this be heard,
Some do it with a bitter look,
Some with a flattering word,
The coward does it with a kiss,
The brave man with a sword!

And yet again, this is something that will show up in fantasy on occasion, but which authors simply refuse to follow through to the end. The hero mercy-kills his best friend; he doesn’t do it on purpose, and he has other loved ones, often a spouse or children, waiting for him at home. He plays a critical part in the destruction of his kingdom, but he survives to flee to a new home, and in time comes to love that home better. His love dies in his arms as the result of a quest they went on, but in the next book he’ll love someone else, who will live.
For maximum raking of the claws across his soul, have him kill the thing he loves with eyes open, no mitigating circumstances, and no softening afterwards that makes it seem as if the killing was for the best.
This is one of those things that has to be handled delicately (well, really, all of these suggestions do). The temptation to spare the hero the suffering this one causes is immense. Your mind will probably start tying itself in knots, specifically trying to do so, and the shortcut might even offer possibilities that having him kill the thing he loves won’t.
But it won’t cause the same amount of pain. And pain is what you’re here for, right?
Not sure what the next rant will be, yet, as the poll seems quite varied.