In RBY - Snorlax followed closely by Farfetch'd.
In GSC - None really.  Didn't complete the game and was kinda falling out of the franchise because I didn't like the selection of pokemon compared to RBY.  It just didn't feel quite right.  Miltank, Smeargle, and Misdreavus were well liked though.
In RSE - Didn't play this series, but still have favorites.  Mawile and Gardevoir tie, followed by Zangoose, Spinda, and Milotic.
In DP - Started playing again.  Lopunny, Mismagius, Toxicroak, and Lickilicky all kind of tie.
Notice a trend?  I am a big fan of Normal types.