Wow! If albums by people such as The Lonely Island and the Foos didn't make it, then the ones that did end up making it have to be really fantastic! I expect that to be the case, as you have good taste, Ke!
40. The Antlers - "Parentheses"
39. Skylar Grey - "Dance Without You"
38. Archeo - "Mr. General"
37. Junior Boys - "Banana Ripple"
36. The Sound of Arrows – "Nova"
35. Lil Wayne ft. Drake - "She Will"
34. Fountains of Wayne - "Richie and Ruben"
33. Peter Bjorn and John - "Second Chance"
32. Mat Kearney - "Ships in the Night"
31. David Dallas – "Take A Picture"
"Richie and Ruben"!!! That's really one of my favourite songs of the year. I never heard their album beyond that, but that's such a great little song. I'm very happy you included it!
I also really like Wayne/Drake, PB&J. A lot of those artists are ones I know (such as Junior Boys, The Antlers, Mat Kearney), but I haven't heard those songs you've listed. I ought to give them a shot!