I'm sure there's a thread akin to this somewhere, so if I'm repeating, I am confident the mods will swoop down and rightfully chastise me.  Everyone who has watched a lot of dorama has probably thought about this topic at some point.  Anyway, here are my choices in the four standard categories for best performances.  
Best Performance by an Actor in a Lead Role
Win:  Masahiko Tsugawa in Aoi--Tokugawa Sandai (2000)
Place:  Kankuro Nakamura in Genroku Ryoran (1999)
Show:  Sanma Akashiya in Sora Kara Furu Ichi-oku no Hoshi (2002)
Best Performance by an Actress in a Lead Role
Win:  Eri Fukatsu in Sora Kara Furu Ichi-oku no Hoshi (2002)
Place:  Tomoko Yamaguchi in Sweet Home (1994)
Show:  Honami Suzuki in News no Onna (1998)
Best Performance by an Actor in a Supporting Role
Win:  Chosuke Ikariya in Odoru Daisosasen (1997)
Place:  Isao Hashizume in Kamisan Nanka Kowakunai (1998)
Show:  Takehiko Ono in Ohsama no Resutoran (1995)
Best Performance by an Actress in a Supporting Role
Win:  Yoko Nogiwa in Sweet Home (1994)
Place:  Shima Iwashita in Aoi--Tokugawa Sandai (2000)
Show:  Shiho Fujimura in Onsen e Ikou (1999) 
It was a challenging but fun exercise in coming up with these choices.  I suspect if I were to do it again in a week, I might make some changes upon more reflection.
Extra Category:  Best Performance by an Ensemble Cast
Win:  Ohsama no Resutoran (1995)
Place:  Odoru Daisosasen (1997)
Show:  Shomuni (1998)