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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Last.FM

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

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You know that you're the reason in everything I do,it's all for you,you know that you're my reason in life,it's all for you...

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
Gas Station Robber
Curious
Meiko
Folio
Adrian Kolbo

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She's in your head, you just don't notice. ♥