Here, asshole. Some of these artists are big, but if they were on a an indie label, so be it. A bunch of others that seemed indie were actually on majors or subsidiaries, and disqualified. Some, like Super Furry Animals, were on and off indie labels, so were occasionally eligible.
1998
1. St. Etienne, Good Humour (Sub Pop)
2. Prince, The Truth (self)
3. Rancid, Life Won't Wait (Dischord)
4. The Jesus and Mary Chain, Munki (Sub Pop)
5. Silver Jews, American Water (Drag City)
1999
1. Pavement, Terror Twilight (Matador)
2. The Dismemberment Plan, Emergency & I (DeSoto)
3. Super Furry Animals, Guerilla (Creation)
4. Underworld, Beaucoup Fish (Junior Boy's Own)
5. Frank Black & The Catholics, Pistolero (SpinART)
2000
1. Sleater-Kinney, All Hands on the Bad One (Kill Rock Stars)
2. The White Stripes, De Stijl (Sympathy for the Record Industry)
3. The New Pornographers, Mass Romantic (Mint/Matador)
N/A
N/A
2001
1. Spoon, Girls Can Tell (Merge)
2. Stephen Malkmus, S/T (Matador)
3. The Dismemberment Plan, Change (DeSoto)
4. My Morning Jacket, At Dawn
5. The White Stripes, White Blood Cells (Sympathy for the Record Industry)
2002
1. Sleater-Kinney, One Beat (Kill Rock Stars)
2. Spoon, Kill the Moonlight (Merge)
3. Tom Waits, Alice (ANTI-/Epitaph)
4. Steve Earle, Jerusalem (E-Squared/Artemis)
5. Wilco, Yankee Hotel Foxrtrot (Nonesuch)
2003
1. Stephen Malkmus & The Jicks, Pig Lib (Matador)
2. The Twilight Singers, Blackberry Belle (One Little Indian)
3. The Postal Service, Give Up (Sub Pop)
4. Death Cab For Cutie, Transatlanticism (Barsuk)
5. Paul Westerberg, Come Feel Me Tremble (Vagrant_
2004
1. The Arcade Fire, Funeral (Merge)
2. Wilco, A Ghost is Born (Nonesuch)
3. Rilo Kiley, More Adventurous (Brute/Beaute)
4. Guided By Voices, Half Smiles of the Decomposed (Matador)
5. Brian Wilson, Smile (Nonesuch)
2005
1. Spoon, Gimme Fiction (Merge)
2. M.I.A., Arular (XL)
3. The New Pornographers, Twin Cinema (Mint/Matador)
4. The National, Alligator (Beggar's Banquet)
5. Frank Black, Honeycomb (Back Porch)
2006
1. Clap Your Hands Say Yeah, S/T (self)
2. Cat Power, The Greatest (Matador)
3. Man Man, Six Demon Bag (Ace Fu)
4. The Format, Dog Problems (Vanity)
5. Islands, Return to the Sea (Equator/Rough Trade)
2007
1. Radiohead, In Rainbows (self)
2. LCD Soundsystem, Sound of Silver (DFA)
3. The Arcade Fire, Neon Bible (Merge)
4. Super Furry Animals, Hey Venus! (Rough Trade)
5. Spoon, Ga Ga Ga Ga Ga (Merge)
2008
1. Los Campesinos, Hold on Now, Youngster (Wichita/Arts & Crafts)
2. Stephen Malkmus & The Jicks, Real Emotional Trash (Matador)
3. Los Campesinos!, We Are Beautiful, We Are Doomed (Wichita/Arts & Crafts)
4. The Raveonettes, Lust Lust Lust (Fierce Panda/Vice)
5. The Dø, A Mouthful (Cinq7)