That's something hard to decide. In sinnoh I had two different teams, because I've played both Diamond and Platinum. In diamond, My favorite would definitely my Garchomp. I have no idea of how many hard battles he fought for me and went victorious. In Platinum, Staraptor has to be my favorite (I also like much my Weavile. Took on Cynthia's Garchomp, Togekiss and Roserade with ease.) His Close combat was like my trumph card to victory. He was so awesome.
In HGSS My fave was my Typhlosion. He's just awesome.