Route 101: Lillipup, Zorua, Sewaddle
Route 102: Lillipup, Gothita, Tympole
Route 103: Lillipup, Chatot, Shellos (not sure which form it is, but it might be West Sea)
Route 104: Pidove, Chatot, Sewaddle
Route 105, 106, 107, 108 and 109: Frillish, Krabby, Skrelp (OR), Clauncher (AS)
Route 110: Trubbish, Chatot, Shellos
Route 111: Sandile, Dwebble, Gible
Route 112: Ponyta, Tyrogue, Throh (OR), Sawk (AS)
Route 113: Scraggy, Klefki, Bouffalant
Route 114: Skorupi, Misdreavus, Tympole
Route 115: Pidove, Misdreavus, Clefairy
Route 116: Pidove, Joltik, Eevee
Route 117: Rattata, Tympole, Deerling (presumably the Spring form)
Route 118: Raticate, Luxio, Aipom
Route 121: Elgyem, Hypno, Aipom
Route 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134: Frillish, Finneon, Alomomola
Meteor Falls: Deino, Druddigon, Clefairy
Granite Cave: Timburr, Axew, Onix
Petalburg Woods: Cottonee, Paras, Phantump
Jagged Pass: Ponyta, Tyrogue, Mankey
Fiery Path: Tyrogue, Diglett, Roggenrola
Mt. Pyre (outside): Growlithe, Bronzor, Elgyem
Shoal Cave: Cubchoo, Dewgong, Delibird
Safari Zone: Kakuna, Pidgeotto, Buneary
Also, note that the DexNav doesn't work in the really tall grass, only the normal grass. Routes 119, 120 and 123 only have really tall grass so that's why those areas have no DexNav encounters.