Fly: Salamence, Rayquaza
Waterfall: Goldeen, Seaking
Rock Smash: Sawk
Whirlpool: Shelder, Mudkip, Wailmer, Wailord, Clamperl, Huntail, Gorebyss, Piplup, Prinplup, Empoleon, Buizel, Floatzel, Finneon,Lumineon, Phione, Manaphy
Rock Climb: Venipede, Whirlipede, Scolipede, Scraggy, Scrafty, Ferrothorn, Druddigon
Source: Used the search bar for the site which tells us which Pokemon learn the move and how.