Hiromoto Sinichi's Perfect Evil, part of Tokyopop's Star Wars manga dealie (basically Tales, but first published in Japan and only as two one-shot anthologies,) was one of those stories that concerned Vader taking on some secret apprentice.
This one, a boy named Tao (whose origins are vaguely Galen Marek-esque,) was soon discovered by the Emperor, who ordered his death. Vader complied with a grievous lightsaber stroke..
..and then took him back to his home planet of Shumari, to drop the body off or something because just go with it.
But then suddenly, out of nowhere..!
( ..Someone with a desire for Vader's head shows up. Two semi-common plot ideas at one blow, then. )