All of these are based on not running back and forth 100 times to do something.

Smart Containers: When you Ctrl-Click a stack into a chest, it will reroute to another chest that already has that item or an item it's grouped with. You can configure the groups if you like but I've never bothered with that.

Show Container Contents: Hover the mouse over a chest to see a list of what's in it.

Auto Fuel: Keep fires, torches, smelters, and kilns full, if what they need is in a nearby chest. "Nearby" can be configured, I keep it short.

Craft From Containers: If what you need for crafting is in a nearby chest, use that. It will use what's in your inventory first.