I'd like to nominate all of the above. I don't think many of these, when included in the plot, are actually thought out very well at all.
Lets start with Amnesia. How can we make this interesting? Well, take an 'amnesiac' that can only remember a few years back. Lets say they're 21 and can't remember anything from before their 18. Later in the story you discover they weren't actually suffering from amnesia, they just have NO MEMORIES AT ALL before that age. Maybe because they're actually some sort of artificial being. Or heck, maybe they're the only one whose memories are actually unaltered, and everyone else has false memories going before that point in time.
All just a dream? Sure, we'll go with that, but do it one better. For the first quarter of the game you were actually trapped in the dream by the REAL villain. Same could go for a game/virtual reality. Or make the point of the plot to actually venture into dreams/games/virtual realities.
Party member obviously going to betray you? It'll be all part of one master plan (one the player is let in on for a change while we're at it) wherein he/she is actually going to betray you, then betray the villain and rejoin you, and this was all planned between the 'traitor' and the main character all along. Or have the main character able to realize this guy is going to betray the party and somehow use that to set him up for a fall. Or have him be a really nice guy and have the least suspicious party member betray you.
Thats just a few ways to spice up these cliches a bit. There's really no idea, no matter how overused, that can't be turned into something more interesting. Thats my opinion. Because once you start taking an idea in a new direction, going back to the old setup becomes more acceptable. If you can trick people into thinking amnesia is never really amnesia in your games, it will actually be a shock when someone actually IS suffering from amnesia.
I guess my real opinion on the matter is that people should think about taking an old cliche in a new direction if they're going to use one at all. And if you successfully turn a cliche into randomly cyclical cliche then no matter how many times the amnesiac princess shows up, people will be forced to think about what is actually in store for them.