Fallout (1) did the Bad Guy repents thing. The first time I played I finally got to the Master, ready to kick his ass with my power armor and plasma rife. Before I could he gets to talking and I find the mutants are sterile and i have proof coversation option. And then the game rocked my world -- the Master saw the error of his ways, and set about to destory what he created (after telling me to get to safety). I was not expecting that at all and it was *immensely* satisfying to think that because I explored the side-paths that lead to learing about the Mutants sterility, (and hanging on to the proof), that I opened up a complely new (and unexpected) resolution to a main goal (based on how I played my character).
 

Hehe... I like it.
 

I like to try and generalize from specific examples as a way to come up with more ideas. Let me propose some broad categories:

The Boss Repents - Subset of "Bloodless Victory." How about giving the players the chance to undermine the Boss's power base, rendering him ineffective?

The Canary Dies - Subset of "Adding Realism" -- give some easy depth to otherwise stale mechanics and let players solve the problems intelligently. Ever see one of these tree-struck witches? They now sell them in miniature form, which doesn't make sense! They're no longer meant to be witches crashing into trees, but iconic representations of witches crashing into trees.

Game dungeons have become iconic representations rather than (call them) simulations of the real thing. Developers generate them based on a checklist (doors? check; keys? check; monsters? check!) rather than by asking themselves, "what would we find down here that might be interesting?" Faced with the "Canary Dies" problem, a player can think about addressing it in multiple ways, be it by making short visits, using a Breathe spell, bringing along a rebreather, or even by skipping that dungeon. Makes me think of "The Ultimate War Sim" and the ramifications of adding some unpleasant realism into a game.

Smaug Invests Wisely - Subset of "Subverting a Trope" -- the players assume something goes according to convention; and it's interesting when it doesn't. In this case, it's not just a negation of a trope (as in "Hit It With A Rock"), but we're taking something and giving it a new basis. (See TV Tropes for a decent list of video game tropes and a better list of TV tropes).

Anyway, Jay's list is good food for thought.
 

Have you ever played The Bard's Tale for PC or console? It may not qualify for all your points, but sure has some funny twists.
 

Planescape: Torment. Seriously. It has several of those(precise accounting withheld as spoiling), and great writing to boot.

Suikoden had a really good big-bad-is-only-sorta-bad twist to it.
 

I don't remember Suikoden's ending anymore. Too many years, the brain starts to go...

I knew Fallout managed to pull off a couple of these. That's part of the reason it's such a classic.

Unfortunately, the company created by the former Fallout team has now gone under. I did play their last RPG, "Vampire the Masquerade: Bloodlines." That one had a few of these little twists in it. Most amusingly, the "It's Just A Rumor" - if you choose the Anarch ending, it is perhaps the BEST RPG Ending Ever. I fell out of my chair laughing. I recommend the game just for that alone.

Unfortunately, the game was fairly buggy, which was also a hallmark of their games...
 

I can't tell you my twist ideas, because they're all a part of the large arc of the Loonyland story that's going to come out over the next few LL games!

What I do in my RPGs is a sort of twist - I implement all the cliches to the limit, but I make fun of them in the process. It's sort of a light parody of RPGs. Why do I keep the cliches in? Because that's fun gameplay. I definitely DON'T think realism is a good thing in games at all. It's just unfun.

The description of the Toughness skill from Loonyland 2:
"With a proper training regimen, anyone can increase their maximum life. That is, they could if there was such a thing as 'maximum life'."

Actually, I'm really proud of the Vampirism skill:
"Don't try to figure out the logic. Hitting guys with your axe has a chance of giving you Life. Just roll with it. Do I come in your house and criticize the curtains?"

There is one problem with true subversion of cliche, like The Boss Repents. There's a very obvious reason why games have big bosses at the end - it's fun, and it's a spectacle. If you ditch that and replace it with an intentional letdown... well, that's a letdown. You can get around that problem by giving the boss a big ultimate demon guardian you have to slay to get to him though, turning the actual boss encounter into a denouement.

In Dr. Lunatic, I have the reverse - when you finally meet up with the evil doctor, you discover (as you might expect from a mad scientist), that he is completely harmless and just runs away from you. But finish him off, and with his dying gasp he dumps zombie brains into his head and becomes Super Duper Zombie Lunatic, a real final boss. That's pretty cliche too, but I've always wanted to have that moment where the wussy evil mastermind is indeed a wussy. Because every time I play a game with a highly intelligent villain instead of a brute beast, I always think "so, how are they going to shoehorn in the final battle?" And they always do - usually he gives you a lecture during which you refrain from hitting him, then hops into a giant machine that makes him all-powerful (I guess I sorta did that with the SDZL, but at least you get to play out the wussy thing first). I can think of lots of good subversions to this, but they're all less of a climax than defeating a giant monstrosity, and therefore bad design. You need the player to end with "I did it!" instead of "oh, that was it."

Anonymous presents a situation that sounds pretty good though - more of a story climax than an action climax. Twists can be good if they're real ingrained and meaningful twists instead of just a deflating joke. I don't know how it's actually done in Fallout, but the good thing for that to do then would be to have a time-pressured chase away from the blast zone to give it the action movie finish - diving out in front of the explosion. Everybody loves that one! Oh, is that a cliche?
 

Well, that's actually the problem - the cliches WORK, and work well - that's how they became cliches in the first place. (Or maybe we can call them a trope, as Dejobaan does, which sounds better and more academic than cliche).

The problem is that from a story perspective, you really need SOMETHING in there. It's like the joke (pointed out in the AWESOME movie "Galaxy Quest") about how all deadly timers in movies and TV shows have to stop with only a second or two left. Disarming the bomb with an hour left on it isn't nearly as exciting! Escapes aren't as exciting unless they are NARROW escapes! Rescues aren't thrilling unless they are in the NICK OF TIME! Victory isn't sweet unless it's against apparently overwhelming odds!

The trick to getting around these cliches is exactly as you say - finding some other twist to bring back the excitement level.

For example: Suppose you are able to negotiate a peace settlement with the big bad Dark Lord. That's right - negotiate. Probably a fun and challenging gameplay exercise if handled correctly, but pretty dissapointing as the climax of the game. You'll have to throw some kind of ringer in at the end (hopefully not just that the Dark Lord has no intention of fulfilling the his part of the bargain - though that's extremely common in real life as well as fiction, to the point of being another cliche). Somehow the stakes have to be raised and a REAL climax has revealed itself. Somehow it's too late, the cosmic upheavals has brought about a greater threat to the world than the Dark Lord, someone is going to disrupt the peace and make things even worse than they were before, etc.

It requires game developers to be sneaky and creative.
 

This was inspired by someone else's suggestions about things they'd like to see changed in RPGs (perhaps even from this blog)... I'd like to design an RPG where the hero/player begins with their full compliment of experience and resources, i.e. the hero immediately following the conclusion of any other RPG. And then it's only downhill from there.

That's the real challenge... the game gets more difficult not because the enemies get stronger but beause the hero gets weaker.
 

Troy - ever play the dice & paper "Call of Cthulhu" game? While you do go up in some stats as you play, your character also goes more and more insane (at least in the earlier editions). In essence, you are on the path to failure from your first stop. Inevitably, your character must either retire, die, or go insane.

The designers did this deliberately to simulate the stories. And the protagonists of the stories almost always ended up pretty crazy.

Anyway - it runs contrary to many player's expectations, and it only appeals to a niche audience (and roleplayers are already niche), but it's got a ... cult following. Pun intended.