I have to second, third, and infinity "He Lives in You" and "Endless Night" for Tobias and Elfangor. When I saw the Lion King for the first time on stage (GO SEE IT ITS AMAZING!) they were the first people I thought of (Even before Simba and Mufasa, haha). Made me tear up a little. :'(
I'll post more as I think of them (Thinking up character songs is like, always running in the back of my brain...all those stupid anime ipod videos, lol.) I'm going to put the videos behind the spoiler screens.
Even though the lyrics don't fit 100%, I think "Be Prepared" is perfect for Visser Three, I could see him singing it.
[spoiler]http://www.youtube.com/watch?v=L0AiN8vrn9Y[/spoiler]
This might be a bit of a stretch, but Disenchanted by My Chemical Romance reminds me a lot of Ax in relation to the Andalites. Mostly from him learning to care for the humans, and then the Andalites writing them off despite his attempts to try to get the Andalites to help them.
[spoiler]http://www.youtube.com/watch?v=nJZhYpXlFls[/spoiler]
For Tobias, I think "Welcome to the Black Parade" fits, talking about how he fights on for his father's ideals even though Elfangor is gone.
[spoiler]http://www.youtube.com/watch?v=-q9q6zl3WIs[/spoiler]