Hard for me to narrow it down too, but I think my all time favourite will always be Bulbasaur and its evolutions, mainly because LeafGreen was the first in the series I played and that was my starter. Lucario is a Pokemon I often use now and has come to be one of my favourites. Few others from each gen:
Gen 1: Pidgeot, Pikachu, Raichu, Nidoking, Rapidash, Charmander line, Jolteon, Dragonite, Gengar, Poliwrath, Alakazam, Venomoth
Gen 2: Totodile line, Espeon, Ampharos, Kingdra
Gen 3: Every starter, Swellow, Flygon, Gardevoir, Manectric, Solrock & Lunatone, Breloom, Glalie, weather trio (favourite legendaries)
Gen 4: Torterra, Infernape, Garchomp, Magmortar, Luxray, Probopass, Magnezone
Gen 5: Serperior, Krookodile, Darmanitan, Chandelure, Haxorus
Gen 6: Fennekin line, Greninja, Goomy, Goodra, Sylveon, Hawlucha