None of them ever do.
Pokemon that have been used by Team Rocket grunts: Zubat, Golbat, Sandshrew, Sandslash, Venonat (only one in Johto's Team Rocket hideout), Machop, Machoke, Drowzee, Hypno, Koffing, Weezing, Grimer, Muk, Ekans, Arbok, Houndour, Oddish, Gloom, Rattata, Raticate, Cubone, Marowak (I think just the one you battle at Mt. Ember).
If you include the scientists, that adds: Magnemite, Magneton, Porygon, Voltorb, Electrode, Ditto.
EDIT: Bulbapedia's trainer listings for Team Rocket Grunt confirms no fossils: http://bulbapedia.bulbagarden.net/wiki/Team_Rocket_Grunt_(Trainer_class)