Definitely Iris. (Though I prefer the New Found Glory cover... :D) And Boulevard Of Broken Dreams even more so... I can relate to that song in so many ways. And Numb too, while I'm on that topic, but I don't think that's particularly 'Aspie'.
My own sort of positive one is Hey Hey by Superchick. It's pretty much a "people might think I'm weird and maybe I'm crazy but as long as I'm myself they don't matter" type of song. So hey hey, this song is for us. So put your hands in the air, if you're crazy like us, hey hey. Otherwise, Boulevard Of Broken Dreams (it is Green Day) is a really good one. (I have no idea how much I've played that song. Repeatedly.) Free by Switchfoot makes me think of Asperger's, sort of, particularly with the line inside this shell there's a prison cell, 'cause that's always how it's felt for me. Never Surrender by Skillet always hit a chord for me... do you know what it's like when you're not who you wanna be? Do you know what it's like to be your own worst enemy? Who sees the things in me I can't hide? Do you know what it's like to wanna surrender? Sober by Pink too, generally around the line, I don't wanna be the girl that has to feel the silence. The quiet scares me 'cause it screams the truth. Going back to the Switchfoot, Mess Of Me makes me think Asperger's too... We lock our souls in cages. We hide inside our shells. It's hard to free the ones you love, when you can't forgive yourself and later, There ain't no drug. No drug to make me well... It's not enough. The sickness is myself. STILL with the Switchfoot, Meant To Live is really Aspie for me. Fumbling his confidence and wondering why the world has passed him by. Hoping that he's meant for more than arguments and failed attempts to fly.
...I'm gonna stop before we all drown in songs.