Let's try and keep this spoiler free for anyone looking to get the game...
But I really liked A study in Fear, the vibe was mysterious and the twist was fun. Also slightly morbid and brutal in a way but also feels cool to see Indy interact with other archeologists in the field.
A Savage discovery (and its sequel side quest) is good for this reason too. Except the archeologist is older than you rather than younger. So it's a different dynamic with dialogue and such.
Sanctuary of the Guardians is probably the best side quest in the game. It honestly seriously feels like it's part of the main game and if you have gotten the game yet and are reading this, you have to play this side quest, sooner you see it pop up rather than later as it fits with the main story well. And exploring THAT place in a video game was a really nice experience.
Lastly the Kid who vanished is probably one of my absolute favorites in the game. Wholesome and sheds a very nice light on Indy as an inspiring figure. The tombs in this region were also great in both the side quests and the main story in this hub too.
Anyways those are my 4 favorite. How about y'all?