I have noticed over the few years of gaming experirnce I have that most games with a somewhat deep plot have running themes or gags. I'm gonna make a list of some of them.

1) The princess isn't here [is in another castle]- the classic "you cam all the way here to save the princess/maiden, but she escaped a few minutes before you got here. So sorry."
2) "You're too weak!"- regardless of how much training and grinding and item collecting you have done, the villain says something along the lines of, "You couldn't POSSIBLY defeat me. Now get out of my way." While you are helpless to watch your uber character get pushed aside.
3) Tedious sidequests- no matter how epic of a quest you are on, someone steps in you're way to force you to do some tedious and menial task that they could've easily done themselves, but instead stop the hero on a quest to SAVE THE EFFING WORLD to go pick up their laundry from the dry cleaners or something. Geez...
4) Yay! We beat the final boss... not- there is always some ssort of FINAL final boss after you kill the "final" boss. Why? Because game developers hate you.
5) Time travel- Lesee here... Chrono Trigger, TLoZ: Ocarina of Time &Majora's Mask, M&L: Partners in Time... yeah.
6) At least one invulnerable enemy- there's always SOME monster in the game you CANNOT kill... geez...

Well, that's all I can think of now, comment if you like or if you think of some more... untill then,

-GS72 out-