The scene in the cottage where Monty attempts to force himself on Marwood. Despite the fact that Monty has just tried to commit rape, the moment where his face moves into the light, and we see that this desperately lonely man has put on makeup to try and make himself more appealing to the much younger and more conventionally attractive Marwood is one of the saddest moments in an incredibly sad film.
Monty's farewell letter to "his boys" is incredibly sad. Even Marwood, despite having nearly been sodomised by Monty the previous night and having spun a quick lie to get away, feels sorry for him.
Marwood(reading the letter aloud): "Perhaps it is just that the eavesdropper should leave as his trade dictates, in secrecy and in the dead of night. I do sincerely hope that you will find the happiness that has sadly always been denied me. Yours faithfully, Montague H. Withnail."
Danny talking about how they've "failed to paint it black" now that the sixties are over and they're selling hippie wigs in shops.
Marwood's fare-well: "I shall miss you, Withnail."
The fact that only a pack of wolves know just how good an actor Withnail can be. Especially that in the original ending Withnail kills himself with a shotgun. As is, the final shot of a despairing Withnail trudging away in the rain, alone, is haunting. The fact that he chooses to recite a monologue from Hamlet suggests that he has come to the same sad realisation that ultimately stopped Monty's acting career: that he will never play "the Dane" on stage.
While not in the film itself, the published script has one in its foreword. In it Bruce Robinson recounts tales of himself and Vivian (the man Withnail is based on) back in the 60s. It's all fun and games until the final paragraph, where it drops the line "And I can't believe Vivian is dead. He got cancer of the throat and they tore his voice out." The rest is absolutely heartbreaking.
