Alisoun cheats on John. Alisoun tricks Absolon into believing she's going to give him a kiss. Absolon tells Alisoun all he wants is a kiss. And in the most elaborate ruse in "The Miller's Tale," Nicholas and Alisoun convince John that a flood is coming and he'd better spend the night hanging from his rafters in a tub. All of the lies and deceit in "The Miller's Tale" happen because somebody wants sex, raising the question of whether it's even possible to come by sex honestly. The only character who doesn't deceive anyone is the somewhat dense carpenter, John, who is also the character most lied to and deceived. Most of the humor in "The Miller's Tale," moreover, comes from our being "in" on this deception.
"The Miller's Tale" is able to make the deceptions that occur in it seem funny, rather than abhorrent, by letting the audience "in" on the jokes before they occur.
The most serious deception that occurs in "The Miller's Tale" is Alisoun's involvement in convincing John to make preparations for the flood, because it betrays the trust between husband and wife.
The most serious deception is Alisoun's prank on Absolon, because it takes advantage of his vulnerability as a scorned lover.
The most serious deception is Alisoun and Nicholas's assertion that John is crazy, because it robs him of his ability to speak and be taken seriously by his neighbors.