Tom Cruise on Tropic Thunder and Johnny Depp in Tusk are two of my favorites where a well known celebrity hid their identity pretty well with voices, prosthetics and makeup, to the point where I wouldn’t have guessed who they were.
Any other good examples.
Matt Damon in Deadpool 2 takes the cake for me. Even after I knew which role he played I had to really look at him before it clicked.
A whole bunch of A listers in The List of Adrian Messenger
Gene Hackman in Young Frankenstein.
Michael Jackson and Dustin Hoffman in the Simpsons.
They didn’t use their real names but you know it was them. 
Jim Carrey cameoed in Liar, Liar, his own movie. He appears as Firemarshall Bill in the background of an ambulance scene.
Robert Downey Jr as the corpse of Sid Shattuck in The Nice Guys.
Cate Blanchett and Peter Jackson in Hot Fuzz
In the Doctor Who series, “Time-Flight,” Anthony Ainley – who had played the Master several times at that point – was unrecognizable in the first episode and was billed as “Leon Ny Taiy” to hide the reveal.
Glenn Close in Hook. She played the bearded pirate who got put into the Boo Box.
Sarah Michelle Gellar in Doctor Horrible. She’s in the audience next to the 3 Captain Hammer fans during the shelter dedication. Wearing sunglasses. At night.
George Clooney voiced the character of Sparky, the gay dog on Southpark. I believed he just barked IIRC.
Dick Van Dyke as Mr Dawes Sr in Mary Poppins. The unscrambling anagram in the final credits suggests that his well disguised second role was intentionally a trick on the viewer.
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Conan O’Brien in How I Met Your Mother.
Parts were. For contractual reasons, Michael didn’t sing in that episode.
Fun trivia note regarding that episode: it’s the reason that FXX is now lying every time they say “Every Simpsons Ever.” Stark Raving Dad - Wikipedia
Also Brad Pitt as Vanisher. You only see him when he meets his demise.
Dang it! Ninjad by eleven hours.
Kevin Costner as the the corpse of Alex in The Big Chill.
Costner was hardly well-known at the time.