My...I can't help but think of starting this same thread a few weeks ago. But
Ok, I'll bite anyway. 

Genesis:
                 "Jesus, He knows me": Done by the 'Children' from Eva,
dressed as Evangelists. 

                 "No Son of Mine": Gendou & Shinji Ikari (It's a little more
than obvious)

                 "Dreaming While you Sleep": Note: This is a VERY obscure
anime video game reference. Yuko Aso from the first of the Valis games. She
ended up killing her best friend and no one knew. 
 
                 "Hold on my Heart": Rick Hunter to Lisa Hayes

                 "Fading Lights": It would orchestrate a better ending for
EVA.

                 "Mama": Shinji Ikari, when his mother dies.

                 "In Too Deep": Yusaku Godai

                 "Tonight, Tonight, Tonight": 8-Man After, (the song is about
drug addiction, take a good guess.)

                  "Brazillian": The very end of Eva. There something so holy
about that song, I don't know why.

                  "I Can't Dance": Almost any anime guy.

                  "Dance on a Volcano": Asuka from Eva, Magma Diver episode
 
                  "Home by the Sea": A fanfic about the beginning of EVA,
where the 'children' go back to the second impact, and it still happens.   

Peter Gabriel:

                "Sledgehammer": Akane Tendou, make Ranma hurt even more. BWA
and Ha

                "Secret World": Washu, she has her subspace lab, so why not?

                "Love to be Loved": Ryoko, strangly enough.

                "Blood of Eden": Change Eden to Jurai and you got a good song
for Ayeka and Tenchi.   

                "Steam": Hotohort from FY, we'll...don't know why, but it
just seems so  fitting.    

                "I Don't Remember": Rei from Eva, well, she's got nothing to
really, remember doesn't she?   

                "Mercy Street": Kiyone, she needs some help after being
stranded thanks to Mihoshi (it was a song dedicated to Anne Sexton, a poet
who had mental problems and killed herself.) 

                 "Big Time": The despisable Captain Tyler (Yeah, don't like
the guy much)

                 "The Voice I Hear": Darien, during the Black Moon arc, his
future self telling him to stay away from Serena.

                 "Shaking the Tree": Tenchi series

                 "I Hold the Light": Kamui, from X

                 "In Your Eyes": Pai, yep, it's in her eyes, all 3 of them. 

Phill Collins:

                  "In the Air Tonight": The storyline from X/1999

                  "I missed again": Yusaku Godai from Maison Ikkoku

                  "A Long Way to Go": Gall Force, any series

                  "Who Said I would": Sayoko from Oh My Goddess

                  "Take me Home": Miaka and Yui from Fushugi Yuugi

                  "Something happened on the way to heaven": Belldandy's
return to the heavens being interrupted by her sisters. And that something is
Keichi.

                  "That's just the way it is": Gall Force, Earth chapter

                  "Dance into the lIght": Sailor Venus

                  "Love Police": Serena, trying her best to live up to being
a superheroine

                  "Wear my Hat": Any male character with multiple love
intrests, be them male or Female.

                  "Cross the River": Slade from Teknoman, or any other "I
don't want to, but I have to" character with a dark past.

                  "Times, they are a changing": From the beginning to the end
of any series.


Can't write anymore, some  of these were pulled out of thin air, others just
might work. I still have more ideas, but can't think of them.

-Warhammer