I'm not sure Ragtime or Titanic would qualify as "underrated". Ragtime won a few Tonys and if it was a financial failure, it received much praise. Titanic did extremely well at the Tonys and was also pretty highly praised at the time, especially considering the negative preopening buzz.
My pics:
Jane Eyre
Bombay Dreams
Parade (though it did walk away with two Tonys)
Once on This Island (a few Tony noms, but the show got lost in season of bigger spectacle hits)
Aspects of Love
Blood Brothers (had a healthy run, but has since been almost entirely forgotten)
"What can you expect from a bunch of seitan worshippers?" - Reginald Tresilian