As you've said, Yoda and Obi Wan were in good when they died, so they disappeared in the traditional Jedi sense of it all. Anakin obviously fell in with the Dark Side and I was always under the impression that Qui Gon was a bit of a rogue Jedi training whom he felt would make good Jedi not taking into account what the Jedi Council told him (they never supported Anakin, remember?)
But another theory has to do with a Jedi's preparedness for death. Qui Gon was slain in battle and this may be the same way many Jedi die in Ep 3. Yoda knew it was his time and accepted his fate. Obi Wan was the same. He did what he came to do and covered while Luke, Han, and Leia escaped. So he resigned himself to his fate and, hence, "disappeared." This wouldn't work for Anakin since he was Sith when he died.