Besides those already mentioned, other interesting things:
A Behanding in Spokane makes it in for Best Play, while In the Next Room, and Superior Donuts do not
No Royal Family for Best Revival of a Play
Performance omissions: Alexander Hanson, Chad Kimball, Quentin Earl Darrington, Christiane Noll, Patrick Breen, Alison Pill and Abigail Breslin, Justin Bartha, Michael McKean, James Spader
Supporting performances that are Tony nomination possibilities who aren’t on the list include Stark Sands, Rebecca Naomi Jones, Sam Rockwell, Kevin Chamberlin, Maria Dizzia, Sarah Paulson
I would assume Everyday Rapture is not eligible (if it is, their system is totally messed up!)
I agree that Brief Encounter is better categorized as a play with music than as a musical.
"What was the name of that cheese that I like?"
"you can't run away forever...but there's nothing wrong with getting a good head start"
"well I hope and I pray, that maybe someday, you'll walk in the room with my heart"