You're asking for the moon here, there's no way I could pick a favorite Björk or Kaki King album.
Homogenic and Dreaming of Revenge are the correct answers.
O:
Anyway, here's mine all alphabetical-wise n' shit (excluding a large number of artists that only have one album, so that takes out almost all of the chiptune stuff)
Alex Mauer - Antarctica
Ataecina - A Tribute to Megadeth
Bass Communion - Loss
Björk - egh, if I
have to pick, I'll take Vespertine
Blackfield - s/t
Bright Eyes - I'm Wide Awake, It's Morning
Casey James and the Staypuft Kid - Transylvania radio
Chroma Key - Graveyard Mountain Home
Coheed and Cambria - The Second Stage Turbine Blade
The Dear Hunter - Act I
Devin Townsend - Ki
Dream Theater - Awake
Explosions in the Sky - All of a Sudden I Miss Everyone
Gregory & the Hawk - Moenie and Kitchi
Joanna Newsom - Have One On Me
Kaki King - Everybody Loves You
Mastodon - Crack the Skye
maudlin of the Well - Part the Second
Modest Mouse - The Moon and Antarctica
My Morning Jacket - At Dawn
Opeth - Watershed
OSI - Free
Pain of Salvation - Remedy Lane
Porcupine Tree - The Incident
Radiohead - OK Computer
Sigur Ros - med sud i eyrum vid spilum endalaust
Strapping Young Lad - Alien
Vampire Weekend - Contra