"Cry,Baby,Cry" on The White Album has a very sinister ambience, & "Happiness Is A Warm Gun" from the same album in which Lennon trawls a net through his own Id & catalogues what he finds there.
And that's before you take into account the horrible new meaning that the title was to take on a dozen years later.
The white album was itself used as a rationale for mass murder. (Though blaming The Beatles for this would be every bit as unfair as blaming J.D. Salinger for Lennon's murder.)
"My Mummy's Dead" from his first proper solo album,very close to home.
Then there's the sheer detachment of his vocals on "A Day In The Life"...
And some people still think of him as a cute head-shaking little popstar.