My 5 favorites are:

Thrice

Permanent Ability

Modest Mouse

Parliament Funkadelic

Franz Ferdinand

3outof5 of your choices i love and adore very much. very nice choices

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wow,i didnt know you love Franz Ferdinand too,under! I love them and cant wait for their new cd.

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i'd have to say:

cursive, american football, gabriel the marine, mineral, and sunny day real estate <3333

'Indie' is such a broad definition incorporating many offshoots of the post-punk era (Britpop, shoegaze, indie rock, lo-fi, etc) and nowadays seems to be some kind of umbrella term for anything with guitars in it that isn't metal...?
But I guess if I was forced at gunpoint to choose a few 'proper' indie groups off the top of my head:

the Smiths
Guided By Voices
The Fall
early Blur
Sebadoh
My Bloody Valentine
the Auteurs
The Jesus & Mary Chain

There are so many denominations of 'indie' (lo-fi, shoegaze, indiepop/C86, indierock etc) that it's a bit difficult to pin down your faves without omitting plenty. That, and the fact that 'indie' these days seems to be an umbrella term encompassing any old **** with electric guitars that isn't metal...?
However if you held me at gunpoint I suppose I'd blurt out these youtube links:

Sebadoh
early Blur
The Smiths
Guided By Voices
The Fall
The Jesus & Mary Chain
My Bloody Valentine
Super Furry Animals

Ingrid Michaelson
Jack Conte
The Shins
Bloc Party
Meiko
Stars
Razorlight

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Barefoot in nightgowns, that's how she dances in the rain. ♥

1. My Bloody Valentine
2. Pixies
3. Silversun Pickups
4. Dinosaur Jr
5. The Smiths
6. Echo and the Bunnymen
7. Radiohead
8. The Jesus and Mary Chain
9. The Stone Roses
10. Slowdive

Nocturnal Emissions
The Dead C
Zoviet France
Shriekback
Pussy Galore
Bobb Trimble

Edit- crap, forgot about 1. The Pastels! how could I forget them.

And the Swirlies.

RILO KILEY
watson twins
decemberists
feist
honeyhoney