If we can go back a little further, I think there are two absolute masterpieces that are tragically underrated:
"Hair" (1979) -- Miraculously, Milos Forman was able to fashion a coherent and compelling narrative, something countless stage productions of this classic have unable to do. He coaxed great, charismatic performances out of Treat Williams, John Savage, and Beverly D'Angelo, among others (including Charlotte Rae!), all celebrating the terrific score -- the movie soundtrack is, to my ears, the best recording of this material ever made. The fantastic choreography by Twyla Tharp (dancing horses!) is just icing on the cake.
"Evita" (1996) -- You can quibble about Madonna being too old for the role, but I think she was absolutely perfect, and her voice was a revelation. Due respect to Ms. LuPone, but her unkind words about Madonna were just dead wrong. But even more pleasing and surprising was Antonio Banderas -- who knew he could sing, dance, and charm the pants off the audience? Alan Parker delivered a great adaptation that should have ushered in a new golden age of movie musicals. It's the movie "Les Miserables" wanted to be.
Honorable Mention:
"South Park: Bigger, Longer & Uncut" (1999) -- Has there been a better original movie score this century? I don't think so. Parker and Stone are geniuses. I just wish they'd work more.