If you look at the source Jhnfui got, here are the list of Pokémon in XY with a 1% encounter rate.
Abomasnow- Route 17
Flabebe White Flower- Routes 4 and 7
Lapras- Route 10 and Azure Bay while surfing
Pumpkaboo Super Size- Route 16 in the tall grass
Rotom Forms (not base form Rotom)- Lost Hotel and Shaking Trash Cans on Tuesday (if you look at the source, the answerer isn’t sure if this is a 1% encounter rate, it’s assumed)
Hope this helps! :)