I'm not much a fan of Webber, but when Murray Head kicks in to "I Don't Know How to Love Him" during "Judas' Death" on the original album, it's probably the most effective dramatic moment I've heard in a Webber recording.
Also, "Tonight" in West Side Story, if we count the Quintet/Chorus as a Reprise, has to be mentioned.
Some other ones I don't think have been mentioned yet, "Forever Yours" in Once on This Island (heart-wrenching), "I Am the One" in Next to Normal, "Look Over There" in La Cage, "Take Me to Heaven" in Sister Act (an altogether forgettable show, but a rather fantastic Act I Finale, that) and, for something completely different, the Lady of the Lake's rendition of "The Song That Goes Like This" in Spamalot, but that might only be because of Sara Ramirez...
I'll also second "Waitin' for the Light to Shine," "One," "Not a Day Goes By" (so incredibly heartbreaking) and, of course "I'll Cover You."
Words don't deserve that kind of malarkey. They're innocent, neutral, precise, standing for this, describing that, meaning the other, so if you look after them you can build bridges across incomprehension and chaos. But when they get their corners knocked off, they're no good anymore…I don't think writers are sacred, but words are. They deserve respect. If you get the right ones in the right order, you can nudge the world a little.