Considering that the Pop year-end chart was sent to the AT40 staff directly from Clear Channel (go check that thread - there's a letter posted in there), I can only infer that there's absolutely no correlation between the year-end or decade-end chart and the weekly charts themselves.
Thus, anyone being left off the chart when they really should be there adds up to nothing more than a steaming pile of bulls**t on the part of Clear Channel, which I'd say is merely par for the course.
So Clear Channel probably just threw this together (although the #1 song was feasible, as it spent 20 weeks at #1). But other than that...
Anyway, I just put together what I consider to be a more accurate listing. It's very evenly balanced, with four songs from each year (according to weeks at #1), and one song per year per quarter of the chart. Here's what I came up with:
1) Wherever You Will Go/The Calling (2002)
2) Unwell/Matchbox Twenty (2003)
3) How To Save A Life/The Fray (2006)
4) Photograph/Nickelback (2005)
5) Smooth/Santana f/Rob Thomas (2000)
6) This Love/Maroon 5 (2004)
7) Bubbly/Colbie Caillat (2007)
8) You Found Me/The Fray (2009)
9) Drops Of Jupiter (Tell Me)/Train (2001)
10) Bleeding Love/Leona Lewis (2008)
11) Here Without You/3 Doors Down (2003)
12) Complicated/Avril Lavigne (2002)
13) Everything You Want/Vertical Horizon (2000)
14) Bad Day/Daniel Powter (2006)
15) She Will Be Loved/Maroon 5 (2004)
16) Use Somebody/Kings Of Leon (2009)
17) You And Me/Lifehouse (2005)
18) Home/Daughtry (2007)
19) Love Song/Sara Bareilles (2008)
20) Thankyou/Dido (2001)
21) Bent/Matchbox Twenty (2000)
22) The Game Of Love/Santana f/Michelle Branch (2002)
23) The Reason/Hoobastank (2004)
24) Boulevard Of Broken Dreams/Green Day (2005)
25) I'm With You/Avril Lavigne (2003)
26) It's Not Over/Daughtry (2007)
27) I'm Yours/Jason Mraz (2008)
28) Second Chance/Shinedown (2009)
29) Hanging By A Moment/Lifehouse (2001)
30) Black Horse & The Cherry Tree/K.T. Tunstall (2006)
31) If You're Gone/Matchbox Twenty (2000)
32) Lonely No More/Rob Thomas (2005)
33) Why Don't You And I/Santana f/Alex Band (2003)
34) Soak Up The Sun/Sheryl Crow (2002)
35) Big Girls Don't Cry/Fergie (2007)
36) Viva La Vida/Coldplay (2008)
37) You're Beautiful/James Blunt (2006)
38) Follow Me/Uncle Kracker (2001)
39) Gotta Be Somebody/Nickelback (2009)
40) My Immortal/Evanescence (2004)
The charts I used were the R&R charts (and Billboard charts starting in August, 2006) since I didn't really feel like going back and checking all the AT40 or Mediabase charts. I took the four songs that spent the longest time at #1 each year and ranked them accordingly. To balance the chart out even more, each quarter of the chart contains one song per year. That will account for songs that spent double digit weeks at #1 (such as "If You're Gone" and "Lonely No More" being ranked low on the charts, while songs that spent less than ten weeks on top (i.e. "Thankyou" by Dido) are way up in the Top 20. I felt this was a fair way of ranking the charts, since nowadays, songs are not spending anywhere near as many weeks at #1 as they were in the early part of the decade.
The year assigned to each song was determined by what year it spent its first week at #1, in case of songs that spilled over into the following year (and the holiday weeks were counted, even in the years of R&R, which did not count the holiday break when figuring the year-end charts). That was how "Wherever You Will Go" ended up on top, as it actually spent 22 weeks at #1 - but it would have won out anyway, as it spent more weeks on the chart than "Unwell". Speaking of "Wherever You Will Go", I sort of bent the rules with that song. You see, it did first hit #1 in 2001, but if I were to list it with that year's songs, there wouldn't have been enough #1 songs in 2002 to work with (and I wanted the list to consist solely of #1 songs), so that was the only such case. All other songs that were #1 between years were assigned the first year that they reached the #1 position.
Yeah, I thought it was totally wrong that big #1 songs like "Photograph" and "Bubbly" were omitted from the AT40 list (at least they played those songs as extras, but still). That was what inspired me to come up with the list above.