Oranges, I'm sure it's happened more than once, but off the top of my head, I know that Chicago won Best Revival without having won Best Musical.
Also, while it's an uphill battle to be nominated when your shows have already closed (moreso on the musical side), I'm sincerely hopeful that Benjamin Walker and Joshua Henry land nominations come Spring. Unless of course there are five better performances than theirs, but...I don't see that happening.
And we're getting a little technical here, but Porgy and Bess, On Your Toes, Anything Goes, Carousel, Show Boat, and Annie Get Your Gun won Best Revival but did not win Best Musical because the Tonys weren't around yet.
And, of course, Assassins, which won Revival but the original production was off-Broadway.
"Art, in itself, is an attempt to bring order out of chaos."-Stephen Sondheim