IMPORTANT: This answer only discusses the base game (in which I have 100%) as I didn't come around to play the DLCs yet.
Now you need to understand something essential: Dark Souls would never stop you from killing NPCs, and quests aren't always very clearly cut, nor do you have a way of looking them up in-game. The only real exemption are those with which you can achieve a different ending (aka a different 10-seconds cut-scene after the last boss).
Some of them have interesting weapons/armor/spells as reward, but I'd honestly suggest you to simply play and not take the fun out of it by reading it up on the Internet. Nothing really comes close to the feeling when you actually go through an interesting quest-line without knowing what comes next.
Honestly the biggest downside of killing NPCs is probably that some merchants will force you to pay more.
NPCs you can kill (excluding merchants + Quest relevant):
the nice giant in Undead Settlement
Ludleth of Courland (the last remaining Lord of Cinder)
Emma, High Priestess of Lothric Castle (not suggested, you will see later)
Eygon of Carim
However, don't fret if you already killed some of them: you probably already broke a lot of more quests and you can't do them all in one run (anymore) anyway. Also, you will be able to buy the armor of many NPCs after killing them from the Shrine Handmaiden.
Additional Fun-Fact (Spoiler):
Every one I listed will turn up dead anyway