1) Never take all items, or store all junk. Just spam the trigger to do it one at a time.

2) Transfer settlement inventory at crafting stations, not a workbench. Only touch a workbench when required, save beforehand as a precaution.

3) Always turn off the pipboy light before raising the pipboy to your face to look at it.

4) If you have the Idiot Savant Perk and it triggers a few times during a crafting or cooking session, stop crafting and let the queued sound effect play. The more of these piled up in the sound queue, the more likely a crash will occur when you exit crafting.

5) Avoid late game instability and bloating of the save file by not dropping items all over the wasteland. Deposit junk in dead NPC bodies so it gets removed from the game world.

6) Do not enter Malden Drainage (just north of Taffington Boathouse) unless you are going to successfully hack the advanced terminal inside, otherwise you'll poison your save file with a bug that causes bullets to eventually do no damage.

7) Building at settlements can cause crashes for users, but different users report different repeatable triggers for a crash. If you ever crash while settlement building, start a habit of saving before doing whatever you did that caused the crash for you.

8) Your game will freeze if you get hungry, thirsty or tired (survival mode) while in VATS. Either avoid it or download the mod to fix it.

9) Don't build in interior bases (Diamond City Player Home or vault 88), or download the fix for interior navmesh cuts (see https://simsettlements.com/site/index.php?threads/major-new-fallout-4-bug-discovered-shared-interior-cell-navcutting.26755/ )
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Performance tip: Turn on your XMP in BIOS. While most games get almost no benefit from running RAM faster, Fallout 4 is the exception. XMP won't run your RAM faster than your motherboard and RAM manufacturer recommend.