Surfing on the Internet I've found a musical Webzine from Chile. The best albums of 2006 are in http://www.super45.cl/2006/12/21/los-45-mejores-discos-del-2006/

The list:
1. JUNIOR BOYS “So This Is Goodbye”
2. YO LA TENGO “I Am Not Afraid of You and I Will Beat Your Ass"
3. DESTROYER “Destroyer’s Rubies”
4. THE RADIO DEPT “Pet Grief”
5. GRIZZLY BEAR “Yellow House”
6. LIARS “Drum’s Not Dead”
7. MOGWAI “Mr. Beast”
8. JAVIERA MENA “Esquemas juveniles”
9. BEIRUT “Gulag Orkestar”
10. CAT POWER “The Greatest”
11. BELLE AND SEBASTIAN “The Life Pursuit”
12. THE DECEMBERISTS “The Crane Wife”
13. CALEXICO “Garden Ruin”
14. JOANNA NEWSOM “Ys”
15. SONIC YOUTH “Rather Ripped”
16. THE KNIFE “Silent Shout”
17. GNARLS BARKLEY “St. Elsewhere”
18. I LOVE YOU BUT I’VE CHOSEN DARKNESS “Fear Is on Our Side”
19. CSS “Cansei de ser sexy”
20. THE RAPTURE “Pieces of the People We Love”
21. SHE WANTS REVENGE “She Wants Revenge”
22. SCOTT WALKER “The Drift”
23. CAMERA OBSCURA “Let’s Get Out of This Country”
24. YEAH YEAH YEAHS “Show Your Bones”
25. SUBTLE “For Hero: For Fool”
26. JUANA MOLINA “Son”
27. GIRL TALK “Night Ripper”
28. BENEOIT PIOULARD “Precis”
29. TV ON THE RADIO “Return to Cookie Mountain”
30. DIVINE COMEDY “Victory for the Comic Muse”
31. GUITAR “Tokyo”
32. FAT JON & STYROFOAM “The Same Channel”
33. RATATAT “Classics”
34. NEKO CASE “Fox Confessor Brings the Flood”
35. MOJAVE 3 “Puzzles Like You”
36. PETER BJORN & JOHN “Writer’s Block”
37. GOSSIP “Stand in the Way of Control”
38. THE STROKES “First Impressions of Earth”
39. SPANK ROCK “YoYoYoYoYo”
40. HOT CHIP “The Warning”
41. BONNIE ‘PRINCE’ BILLY “The Letting Go”
42. THE DRIFT “Noumena”
43. PSAPP “The Only Thing I Ever Wanted”
44. NATURAL SNOW BUILDINGS “The Dance of the Moon and the Sun”
45. CURRENT 93 “Black Ships Ate the Sky”

Cool!

Do they have lists from previous years as well? It's a bit difficult for me to navigate with my very limited Spanish...

Well, it seems that it’s a webzine going on from 1996, and there are lists from 2000, but I couldn't find them, except the top 10 of 2005:
1. LCD SOUNDSYSTEM “LCD Soundsystem”
2. BLOC PARTY “Silent Alarm”
3. SUFJAN STEVENS “Illinois”
4. FRANZ FERDINAND “You Could Have It So Much Better”
5. CLAP YOUR HANDS AND SAY YEAH “Clap Your Hands and Say Yeah”
6. DEVENDRA BANHART “Cripple Crow”
7. ANTONY AND THE JOHNSONS “I Am a Bird Now”
8. EDITORS “”Back Room”
9. BROADCAST “Tender Buttons”
10. OF MONTREAL “The Sunlandic Twins”

http://www.super45.cl/2006/01/02/los-45-mejores-discos-del-2005/