While in play, Mysterious Fossil, Claw Fossil, and Root Fossil, count as both Trainer cards and as Pokémon. Previous rulings did not consider them to be "Trainer cards" while in play.
Source: PUI Announcement (2005-04-05), PUI Rules Team (2005-04-07)

Relevant cards

Note: All applicable cards may not be listed below.
EX2_90
EX2_91
EX2_92
WOTCFO_62
WOTCLC_109