Signal Fire, an very emotional and great song.
Out of all three?
Hero.
Just b/c it takes me back to 2002, when Spider-Man was coming out, and it was such an amazing summer...and great time in my life, skipping school to see the movie for the first time. Then seeing it again that night with my g/f.
Vindicated though, is a great song too and really connects w/ Spidey 2, it would of probably been a better song in the long run for 3 though.