The term "stakes" also refers to what is won or lost during Conflict Resolution. As in, Conflict: Do you talk him out of committing the murder? The stakes are: "Does he murder her or not?"
The stakes might also be: "Does he try to murder her or not?", which is one reason why it's valuable to set them beforehand.
Most games that have stake-setting allow the player to back out of the roll when they find out the stakes. This helps avoid cruel GM behavior such as:
Player: I climb down the cliff.
GM: That'll be difficulty 5. Roll it.
Player: What? I thought it would be much easier than that.
GM: It's a sheer cliff face! Roll it!
Player rolls, gets injured, and seethes because his character just did something he "wouldn't really have done."
With stakes-setting, this becomes:
Player: I climb down the cliff.
GM: Ok, that'll be difficulty 5, if you succeed, you make it down. If you fail, you'll fall and be injured.
Player: What? I thought it would be much easier than that.
GM: (Shrugs) It's a sheer cliff face.
Player: I'll try to find another way down.
Stakes Considered Harmful?
Stakes originated as a way of expressing what players actually intended to achieve through their actions — in other words, as a reaction to accidental or willful misinterpretation on the part of whoever had plot authority. These examples are yet again paraphrased from Vincent Baker's work:
PLAYER: I bust into the safe!
GM: Why?
PLAYER: To get the dirt on the supervillain!
GM: OK. Roll to see if you bust into the safe.
PLAYER: *rolls* Success!
GM: OK. You bust into the safe. But the dirt on the supervillain isn't there.
(Some say the above is an example of why the intimate factual details of any setting must always be predetermined; that addresses the problem of deliberate blocking of player intent, but not that of aimless and frustrating play.)
By Setting Stakes — that is, by making clear the intent behind character actions even if the game rules do not then necessarily grant all of that intent (which is to say, even if the game does not use conflict resolution as opposed to task resolution) — players can avoid that specific problem. However, some believe that many rulesets that make explicit use of stakes take them too far, and destroy something important in the process.
PLAYER: I bust into the safe!
GM: Why?
PLAYER: To get the dirt on the supervillain!
GM: OK. Roll to see if you bust into the safe.
PLAYER: *rolls* Success!
GM: OK. You bust into the safe. But the dirt on the supervillain isn't there. So, say how you get the dirt on the supervillain.
PLAYER: Uh… I lead a months-long campaign of investigation deep in the corridors of City Hall, making use of my every contact.
In the above example, the final line summarizes a wide swath of fiction that could have made for a substantial amount of satisfying play. Some call this "playing before you play," or simply say it breaks the boundaries of the scene/situation. ("Situation" is defined here as "characters + a setting." When you look at characters and setting in the context of one scene, it's easy to see where the boundaries of the situation are.)
Be careful not to do this when setting stakes. Also, be careful to set stakes in the way that the rules actually indicate - there's usually a good reason for the indication, and the reason often has to do with the above. Several games famous for including stakes, such as Dogs in the Vineyard and Primetime Adventures, frequently see complaints from players about imperfect play sessions wherein stakes were used in a way the designer didn't intend. (As far as the two cited games, no "opposing stakes" are intended to be set.)