Ways of repelling/ decreasing encounter chances:
i. Repel, Super Repel, Max Repel (item)
ii. Cleanse Tag (item)
iii. Stench - decreased by 50%
iv. Snow Cloak - decreased by 50% (only in a blizzard)
v. Sand Viel - decreased by 50% (only in a sandstorm)
vi. Quick Feet (couldn't find percentage)
vii. Keen Eye and Intimidate - decreased by 50% (lower level Pokemon are encountered less often)
viii. Pure Incense (couldn't find percentage)
ix. Black Flute (couldn't find percentage) (only in Gen III to Gen IV)
Since I went through all abilities, I thought I might as well add the ones that increase/ influence encounter rates.
Ways of increasing/ influenceing encounter chances:
ii. Suction Cups (fishing only)
iii. Sticky Hold (fishing only)
iv. Synchronise (increases chance of meeting a Pokemon with the same nature)
v. Static (attracts Electric types)
vi. Pressure, Vital Spirit and Hustle increase chances of meeting a higher leveled Pokemon
vii. No Guard
viii. Magnet Pull (for steel types only)
x. Cute Charm (increases encounter of opposite gender)
xi. Arena Trap
xii. White Flute (only in Gen III to Gen IV)
Note that for all these abilities to work outside of battle, the Pokemon with the ability needs to be leading the party.
I think this is the full list. I'll add if I find anything else.