The list will be longer, and I may miss a few, but here are the ones I know.
Regular grass encounter
Dexnav (ORAS)
Pokeradar
Hoenn Sound (HG/SS)
Sinnoh Sound (HG/SS)
Having a Pokemon game in the GBA slot.
Interaction
Driftveil Drawbridge (There is a shadow on the bridge)
Surfing
Fishing
Rock Smash (Games with Rock Smash as an HM)
In a cave
Headbutt (G/S/C and HG/SS)
Honey Tree (D/P/Pt)
(Credit to Sapph on these next 7)
Trash can
Falling from ceiling
Jumping out from a bush
Walking into a shadow
Jumping out from snow
Seaweed
Soaring into a flock of birds (ORAS)
Hoard (Does that count?)
Honey (Gen 4 and up)
Sweet Scent (Gen 2 and up)
Walking in deep sand (Credit to sumwun)
Walking in swampy water
Walking in Flowers in X/Y (Credit to sumwun)
Abandoned Buildings
Phenomenons (B/W and B2/W2)
Stepping on a Pokemon (X/Y)
I think I got most, if not, all of them.
Source
