Sadly, Christopher Eccleston (the 9th Doctor) will not be making an appearance in the Doctor Who 50th Anniversary episode, but his voice will be in an episode.
In the episode Journey to the Centre of the TARDIS, Eccleston’s voice as the Doctor (from the episode Rose) will be played as a voice-over in a scene that shows a space salvage team attempts to break into the TARDIS.
The assembled hordes of Genghis Khan couldn’t get through these doors, and believe me they’ve tried.
Of course, there will be no new scenes featuring Eccleston for any episode, including the 50th anniversary episode. Only David Tennant (10th Doctor) and Billie Piper (Rose Tyler, the 9th and 10th’s companion) have been confirmed to appear in the anniversary episode, as far as we know.
Well… It’s better than nothing.
Doctor Who’s Journey of the Centre of the TARDIS is set to air on April 27th on BBC One/America.