OK...keeping in line with the time period defined and sticking with the theme of 'rock', thus leaving out electronica and some of the more pop-oriented material, here's some pretty great indie stuff of recent years. This is by no means intended to be a 'best of' list...just a bunch of cool sounds.
1) Califone: 'Roomsound' + 'Califone (EP)'
2) Yo La Tengo: 'Painful' + 'I Can Hear the Heart Beating as One'
3) The Walkabouts: 'Train Leaves at Eight' + 'Satisfied Mind'
4) Giant Sand: 'Chore of Enchantment'
5) Edith Frost: 'Calling Over Time' + 'Wonder Wonder'
6) David Kilgour: 'Feather in the Engine'
7) Calexico: 'The Black Light'
8) Do Make Say Think: 'Goodbye Enemy Airship, the Landlord is Dead'
9) The Beta Band: 'Three EP's'
10) The Brian Jonestown Massacre: 'Take it From the Man'
11) Brother J.T.: 'Rainy Day Fun'
12) Cul De Sac: 'Crashes to Light, Minutes to it's Fall'
13) Eleventh Dream Day: 'Eighth' + 'Ursa Major'
14) Neutral Milk Hotel: 'On Avery Island' + 'In the Aeroplane Over the Sea'
15) Low: 'Things We Lost in the Fire'
16) Songs Ohia: 'Didn't It Rain' + 'Electric Magnolia Co.'
17) Stereolab: 'Transient Random Noise Bursts with Announcements' - cheating a bit on this one, since it did come out on a major label on these shores
18) Neu!: (reissues) - yeah, I'm cheating on this too (early '70's recordings), but I felt like I gotta mention it
19) Dirty Three: (many recordings)
I could probably add some to this already too long list(and delete a couple), but there's my rambling list of the moment. This is of course all IMHO and YMMV, etc.
