I'm not really sure. The Alakazam line would be a fit choice since I've always liked it since Gen I, and enjoyed training them in different gens. Same with Tyranitar in Gen II and the Cradily line in Gen III. I've always enjoyed using them and I've recently bred and trained them again in Gen V. There are a lot of other Pokémon I love, old and new, but I think that these three will always remain in a special place and thus they would classify as my "signature Pokémon".