Excellent question! I did some research and this is what I came up with...
Arena Trap, Illuminate, No Guard, Swarm: more likely to encounter wild pokemon
Quick Feet, Stench, White Smoke: less likely to encounter wild pokemon
Sand Veil: less likely to encounter wild pokemon, if you are in a sandstorm
Snow Cloak: less likely to encounter wild pokemon, if you are in a snowstorm
Static: more likely to encounter Electric-type pokemon
Magnet Pull: more likely to find Steel-type pokemon in the wild
Intimidate, Hustle, Keen Eye, Pressure, Vital Spirit: increases the chance of encountering a higher-level pokemon
Compoundeyes: more likely to encounter pokemon holding an item
Synchronize: 50% chance of encountering a pokemon with the same nature
Cute Charm: 66% chance of encountering a pokemon with the opposite gender
Sticky Hold, Suction Cups: higher chance of getting a bite when fishing
Pickup: the pokemon may pick up items
Honey Gather: pokemon may pick up honey
Flame Body, Magma Armor: halves the number of steps needed to hatch an egg