Indiewood might be a better moniker here than Indie but at any rate, here they are via the wonderful compilers at Indiewire.

Top Grossing Independent Films of the 2000s

1. The Passion of the Christ, 2004 (Newmarket)  $370,274,604
2. My Big Fat Greek Wedding, 2003 (IFC Films)  $241,438,208
3. Juno, 2007 (Fox Searchlight)  $143,395,265
4. Slumdog Millionaire, 2008 (Fox Searchlight)  $141,319,928
5. Crouching Tiger, Hidden Dragon, 2000 (Sony Pictures Classics) $128,078,872
6. Traffic, 2000 (USA) $124,115,725
7. Fahrenheit 9/11, 2004 (Lionsgate) $119,194,771
8. Paranormal Activity, 2009 (Paramount)  $107,753,000
9. Brokeback Mountain, 2005 (Focus Features)  $83,043,761
10. March of the Penguins, 2005 (Warner Independent) $77,437,223
11. Coraline, 2009 (Focus Features)  $75,286,229
12. Sideways, 2004 (Fox Searchlight)  $71,503,593
13. Burn After Reading, 2008 (Focus Features)  $60,355,347
14. Little Miss Sunshine, 2006 (Fox Searchlight)  $59,891,098
15. Crash, 2005 (Lionsgate) $54,580,300
16. Atonement, 2007 (Focus Features) $50,927,067
17. 28 Days Later, 2003 (Fox Searchlight)  $45,064,915
18. Lost In Translation, 2003 (Focus Features)  $44,585,453
19. Napoleon Dynamite, 2004 (Fox Searchlight)  $44,540,956
20. Precious: Based on the novel ‘Push’ by Sapphire, 2009 (Lionsgate)  $42,432,006