And I also forgot the Star Trek Online/Nu-Trek stuff. Like Thrawn
said, if you're going to read The Needs of the Many
it may spoil things in the Lit-verse. But Star Trek Online takes place in an alternate continuity from the Lit-verse so things don't line up except for a few backstory details.
As far as the Nu-Trek comics and young adult novels go they are mostly unrelated to anything else. The prequel comic to the first film may or may not end up in continuity with the Lit-verse. If it does it takes place in the future of the current Lit-verse 'present' and could be considered as spoilers for recent novels.