Why do some Jedi disappear when they die while others don't?
Some Jedi disappear when they die:
In Star Wars Episode IV: A New Hope
At the end of his duel with Vader on the first Death Star, Obi-Wan Kenobi let down his guard and concentrated for a moment, disappearing entirely just as Vader's lightsaber passed through his empty robe.
In Star Wars Episode VI: Return of the Jedi
When Luke returned to Dagobah in the Return of the Jedi, Yoda also disappears when he peacefully dies.
In Star Wars Episode VIII: The Last Jedi
When Luke is exhausted after “being” on Crait he looks into the Horizon and disappears.
And others don't:
Star Wars Episode I: The Phantom Menace
When Qui-Gon Jinn's dies after his duel with Darth Maul, he doesn't disappear and is cremated.
Star Wars Episode VI: Return of the Jedi
When Vader/Anakin Skywalker dies on the second Death Star, he does not disappear and he is cremated by Luke.
Also, they all became a "ghost" after their death.
In the Expanded Universe novels it is shown that most Jedi do NOT disappear upon death. Those who do have 'become One with the Force'.
It is implied that only those who disappear can re-appear as Force Ghosts, but Vader seems to invalidate this (EDIT: Correction - Vader's organic body DID disappear, what was burned was just his suit - see the section on his death, near the bottom.). A better theory is that learning how to become a Force Ghost - a technique Qui-Gonn is said to have rediscovered enables a Jedi who is prepared for death to disappear upon their physical form dying.
To disappear upon death requires great strength in the Force (equivalent to a Jedi Master), great wisdom and understanding of its ways, and for the person who dies to be at peace.
In the movie you can't see whether Vader's body is in the armor or not when it is cremated, and while the link you have above says the body disappeared there is no reference for that information. Is this detail given in one of the books or comics?
Not that I'm aware of, but the Wookiepedia is linked to from Darth Vader's character profile on starwars.com - that's a pretty strong endorsement.
I think this was the 3rd greatest blasphemy that was inflicted upon us in the e1-3. In the original RoTJ Vader did not fade away after death. The Second being midiclorians and of course the first being JarJar.
There wasn't much of Vader left to disappear, too. His legs were gone, an arm, most of the other arm...he was more machine than man after all his cybernetic replacements were in place.
@Bart Silverstrim - That's true. Then Vader's so called "ghost" should be without his arms & legs.