Usually for every Zelda game, its fighting the Bosses at the end of each temple/level as well as the final boss, only if the final boss is seen in the one game (exceptions do apply like Vaati from Minish Cap, being seen as the Wind God or whatever it was in the Multiplayer version of the four swords).
Apart from that:
PH - Duo moving (or switching between) with the Goron guy.
MC - Getting the Mole Mitts (Awesome thing when digging), giving the shield to biggoron to eat before you get the mirror shield and the two different views of the game, being minish or normal.
WW - Switching between, forget her name but she has this harp and flys.