The mention of Mormonism as one of the religions that will "spill theirs just anywhere" in "Every Sperm Is Sacred" was ironically funny to those in the know at the time, since the publicly expressed attitudes of senior church leaders towards birth control were almost identical to the Catholic view (for different theological reasons, though). In recent years, however, the LDS Church has clarified its birth control position, stating that couples aren't restricted from using contraception, thus making them (slightly) more lax on the topic than Roman Catholicism.
Nowadays, people will say that Graham Chapman wearing the corset and white wig in "Find the Fish" reminds them of Lady Gaga.
Mr. Creosote serves as this both within and without the film. With the bath tubs of dairy based vomit FX going off by day three or so of shooting, he even began to affect the filmmakers themselves... In fact, if you look closely after he explodes, you can actually see several extras actually throwing up as they leave.
The final shot of the film, arguably: Michael Palin (in drag, of course) has just finished up a rambling and bizarre speech about film censorship, when the Flying Circus theme music begins to play, loud and clear. The film suddenly cuts to the beginning of a Flying Circus episode playing on a TV set, pulling away from the camera to reveal that it's floating around in space. It then flies off into space, and the end credits roll. An appropriate way to end Monty Python itself, and more than a little moving if you're a big Python fan.
Seeing Graham Chapman in the Colonel getup one last time.
The soldiers preparing a party for their commanding officer, all the while getting shot at.
The Catholic children all being marched out of their home, tearfully singing "Every Sperm is Sacred". Then you see them in heaven. That's right. Their devout Catholic father sent them to their graves, all because he wouldn't wear a condom or get a vasectomy.