Pretty much 75% of my top favorite series list is from Nintendo, so I'll just exclude it altogether. I really love Assassins Creed. Characters, story, music, etc. Combat can get repetitive but I always loved it.
Hard to say, I love Mario of course. I also love Final Fantasy I-IX. X was OK though.
I would probably say however it's Grand Theft Auto. I think it's a brilliant series and I've logged hours and hours of entertainment from it. And say what you will I think it is actually very well-written. I've loved a lot of the characters and hilarious radio personalities. Rockstar's humor is unmatched in the video game industry imo.
Kingdom Hearts 2. I had never played Kingdom Hearts one when I played it, but the game was standalone enough for me to still be able to perfectly understand the story. Plus, what little it had of Final Fantasy balanced out the extreme amounts of Disney Characters in it... whole worlds devoted stuff like Winnie the Pooh and Beauty and the Beast, where another world had Sephiroth as a boss...
It's a tie between Pokémon XD: Gale of Darkness and Elder Scroll V: Skyrim
I just love those games. Not as much as Link to the Past/Majora's Mask, but...you know.