Here's your answer to the boss fight question: http://en.wikipedia.org/wiki/Boss_%28video_gaming%29
As for other cliches, here are some:
- fruit as bonus objects
- a girl needs rescuing
- the player is the only person who can save the world from a massive evil force
- in beat'em-ups the enemies are punks/skinheads/junkies/body builders/ninjas/freaks
The reason behind cliches that I can think of is that most games would recycle successful ideas thinking them as selling points for the game. Why else would all the games from a certain period look mostly the same?