Lyrical Dissonance is a very common theme used in numerous Vocaloid songs. In fact, it's harder to find a song which doesn't follow this trope.
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Macaron is a mysterious song with almost poetic lyrics about how a singer enjoys eating macarons.
Many song from Star Girl and The Illusion Paradise series have shades of this trope.
The trope is averted in the first half of The Nun and Idol Girl. At the beginning it's a happy j-pop song about a nun who wanted to be become an idol, and thanks to Dr. Realist, her wish was granted. It didn't end well as the idol got overwhelmed by insults to the point of cutting herself. And then it got much worse. The girl was reminded that such a thing had already happened in reality. After she remembered this, she ran to the church with a knife to kill herself, but she was caught by a priest, who then was accidentally killed by the girl, because she forget to drop the knife and she fatally stabbed him as consequence. She returns to be a nun and constantly pray to God to forgive all her actions, even though she knew he won't.
Breaking Things into Pieces is a happy song about a person, who has a bee in her bonnet about destroying everything, because he believes they are granted a piece of their soul when people become attached to them. It's worth it to add that said things in the title isn't confined only to inanimate objects.
Though Owata-P rarely uses this trope, he has some songs following this theme:
This trope may be averted. Other interpretations of the song say that the main singer is an internet addict trying to socialize online, but his mind is slowly corrupted by it. However he finally tackled how imperfect the virtual world is, so he decided to leave it and start a new life in reality. In this case, the lyrics relate to the virtual world instead.
The whole "Do Vocaloids Dream of Doomsday Birds?" series. Almost every song (excluding ＊Sayonara, World End) has a chiptune or video game-like melody, while the lyrics are about the destruction of mankind and Earth due to war.
The most notable one is ''*Hello, Planet'', sung by Hatsune Miku, being chronologically the last song in this series. It's about Miku, who wakes up after the apocalypse and wanders through a deserted wasteland to find her master. The whole song ends with a happy closing melody in a scene where Miku dies in front of her master's grave.
Numerous songs from the Happiness series. Every one of them has an electronic melody you could dance to, but the lyrics expose its morbid meaning.
In, "An Earnest Unrequited Love, Wanting to Make it Bear a Little Happiness": The song starts with a happy chirpy romantic tune, until Mayu reveals part way that she knows everything about the guy she's crushing on and who's he's dating. Mayu then proceeds to singing about killing her rivals by physically and psychologically maiming them. In the end she decides to kill her crush as well.
Mayu's story seems to be connected to: "You're Seriously Mad? I'm not mistaken here", Where again it starts out in a lovey dovey whimsical tune, until again she sings about stalking then killing her crush, apparently dumping his body in the pool, then quietly clearing off evidence. Surprisingly! Mayu is not a Karma Houdini, because she also sings about getting caught at the start and in the end.
In, "I'm Sorry for Liking You": the tune is an uplifting romance song that is reminiscent of a comedy love genre. It doesn't turns out to be anything but that. IA apparently bought a pair of contact lenses, that can give you laser eyes. When she failed to read the manual, it gets stuck in her eyes. She panics all the while she burns everything she sees to the ground including her crush. However unlike most examples it ends in a Surprisingly Happy Ending.