I don't think that anyone has mentioned it yet, but the most egregious ever is Gypsy vs. Sound of Music and, I seem to recall, Fiorello in a tie. I loved the SOM score, but it ain't Gypsy.
i also don't think anyone has mentioned Purlie or even Coco vs. Applause, whose score was mediocre from the outset, even if I enjoyed the show a couple of times. Purlie has a wonderful, joyous score and I think that Coco is under appreciated, although not every song is stellar.
Couple of other comments:
Hallelujah! Baby! Has gotten trashed by several of you. I personally think it is a wonderful score and am appalled that anyone would even mention How Now Dow Jones, which has exactly 2 good songs, one a comedy number. I love The Happy Time score, but don't think it comes anywhere near Hallelujah! Go back and listen to the score.
I love most Sondheim scores, but totally hate the score for Into the Woods. I find it so repetitive, especially the title song. There are a couple of terrific songs, but Phantom has a slew of them.
Nine is one of my favorite scores ever and the recording of it is amazing, with the last 10 minutes or so being a mini-masterpiece. I loved Dreamgirls, saw it more times than Nine, in fact, but I don't think the score is particularly good, with the notable exceptions of Step Into the Bad Side and And I Am Telling You and maybe I am Changing.
Urinetown's score is terrific. It won the Tony against a much bigger financial hit because the voters thought that it was better, not because of its chances of being a success on the road. I disliked Sweet Smell intensely and have to admit to never listening to the score again, but Millie ain't in the same league.
I agree with Jeffrey K's first three comments comparisons...I only disagree with the last one. I think Finding Neverland was last year's best score, which I know is a mortal sin to say, but there ha go.
Finally, I think She Loves Me should have won in its year, but nothing was gonna get in the way of the juggernaut, Hello! Dolly! score, which was the weakest part of the show IMO, although there are God knows some wonderful songs in the show. Since it was not even nominated, it is moot. And I think Chess should have won in its year, even though I think the Les Mis score is wonderful...I think Chess is one of the best ever.