Mods at the top of the list will overwrite things at the bottom.

If you have a BIG mod, use it as your reference.
Standalone small mods that share resources with it can generally go under it.
Mods that tune things in the big mod need to be above the mod they tune to overwrite bits of it.

* Some mods are not compatible at all, because they sort things in different categories/flags. Best example of that would be The North and Colonial Charter.

** Because flag/categories got reworked in the last Banished patch, mods published before mid 2017 can also cause issues, with items having flags that are now handled differently. Old mods that tweak storage or change the flag of items (like mods keeping coal from being used in houses) should be avoided.

*** Whenever you make a change to your modlist, take the time to entirely exit Banished and restart before you play, or you'll crash when you try to exit your town and get back to the main menu. Not a mod's falt, just an issue with the game poorly recording changes to mod menu.