I (partially) blame tvdb for this mess. SpongeBob has every story listed as a separate episode, but good luck finding any source that doesn’t bundle these up.

Meanwhile, the list for Kaguya just bundles all stories aired together in a single episode (thankfully).

To add some not already mentioned

• Apothecary diaries
• Dan da Dan
• Heavenly delusion
• Puella Magi Madoka

If you don’t mind older series, I think these are worth a recommendation:

• Bakemonogatari (and the rest of Monogatari series)
• The melancholy of Suzumiya Haruhi
• Black Lagoon
• Clannad

Honorable mention for Nichijou. Perfect comedy if you ask me :)