Lord Lucien
Lets all love Lain
Both Jedi and Sith get weaker the closer we get to the Empire, e.g. Ragnos=Best of the Best (but still never fully explained, I like mystery). They start getting stronger after Palpatine dies AT ENDOR WHERE HE STAYS DEAD.
Bane gets credit for Darth.
The events of KoTOR II don't happen. No Exile's wound, no Nihilus Mega-Drain, no invincible Sion.
The Dark Nest series never happen. They've always felt like an unnecessary interval between the NJO and LoTF.
The Legacy comics are scrapped and re-adapted into novels(with pictures). Krayt's order can call themselves Sith all they want, but in truth are really just Dark Jedi.
The only known Sith Lords that exist in the 3000 year period in between The Old Sith Wars and the Brotherhood of Darkness are---NO ONE. No "the Sith rule galaxy," no Andeddu or whoever. 3000 years of mystery.
That's all I can think of for now.