Favourite Starter: Cyndaquil. Purely on merit of its appearance, no logical reasoning.
Favourite Region: Jhoto. I loved the Unown ruins, the thing with the Red Gyarados, and the various towers such as the Bellsprout tower and the one Ho-oh was in. The region as a whole had an "old fashioned" feel imo, especially some of the northern towns.
Pokémon I caught with the masterball: Mew (hax :P), Mewtwo x3, Ho-oh x2, shiny Dratini, Latios, Latias, Deoxys, Giratina, Regigigas.
Favourite pokémon game: Pokémon Mystery Dungeon: Explorers of Time/Darkness. Or if we're sticking with the main series, Emerald. (I haven't played any game past Diamond/Pearl)