Traditionally I have run mostly homebrew adventures. I’ve used encounters taken from commercial adventures every once in a while. The Dragonlance campaign I’m running is the first I’ve really tried to run a module straight.
My players aren’t always going along with that idea but that’s ok. I’ve also added some content because I wanted a special event for the character with divine powers. I plan to do the same for the knight. Due to this I created Dulsi’s Dragonlance Addendum on DMs Guild.
For Spelljammer I found the process less satisfying. I had to tweak many individual encounters to match what I wanted. So running it requires looking at the adventure and looking my notes for things to override.
I find Paizo’s Adventure Path line of products to be really good. I frequently tweak encounters, sometimes brewing my own NPCs for them, and occasionally add my own scenarios to bulk them out or elaborate on something that wasn’t detailed in the AP. The actual stories I don’t often touch, however. I’ve yet to really need to.