Here are some of my favorite Doctor Who episodes, ranked in order of favorite to least favorite. This page WILL contain spoilers for the included episodes.
The Bells of Saint John is my current favorite New Who episode, because it is when the Doctor is introduced to my favorite companion, Clara Oswald.
The two-parter Dark Water/Death in Heaven is my second favorite episode of NuWho because to me it shows how Doctor Who does not stray away from more serious themes, evidenced by the plot of Missy turning many of the dead, into cybermen, including Clara's recently deceased boyfriend, Danny Pink.