I don't tend to use a lot of house rules, and what I do are usually additive then changing some rule. In one of my Traveller games I added a Luck Point system, where if somebody rolled double ones on a skill check they got a Luck Point. Then after another skill check they could spend a point to reroll. You can't spend more than one point on a roll, but more than one person can spend a point on a single skill check to reroll it again. It's been great for player engagement, and has lead to some really fun moments as everybody scrambles to check if they have any points to spend on an important roll. Another one I use in my Traveller games is I added an Overwatch action. Inspired by the Xcom games, you can spend your action on your turn to keep your gun trained on a specific area, and if anybody moves through that area you get a free shot.
I also recently started playing Pathfinder 2e, and though in keeping it rules as written, especially as I learn the system, I have made it so that the party can only level up if they're in Downtime mode, to encourage my players to actually make use of Downtime.