I'd certainly like to see some RE-Released in proper, special features editions - Robots of Death and Pyramids of Mars spring to mind.
I'd quite like a Peladon box-set (presumably including "The Bride of Peladon" on audio), with a proper dissection of the Ice Warriors' place in the Dr Who universe, as a baddie that made good.
Similarly, I'd love a Nestene box-set (Spearhead and Terror), with investigative pieces on how the Nestene/Autons came to be, the backlash about the scariness at the time, the search for the right actor to be the Doctor's "Moriarty" and the casting of Roger Delgado, the whole decision to bring Doctor Who down to Earth for the Pertwee series, and maybe a couple of featurettes - one from Russell T Davies, explaining why he decided to launch the new version of Who with the Nestenes, and one from fans, stars, and other "Masters" on their memories of the Master, and Delgado's portrayal in particular.
I'm probably the only fan on the planet who'd also quite welcome a Trial of a Time Lord box set, but I think the extra features with that could be really quite interesting - feature on the troubled times of the Sixth Doctor, get Michael Grade on to put his case, get Colin Baker on to fully explain what it felt like to be the only Doctor not to decide his own leaving date, get Nicola Bryant on - did she jump or was she pushed into going bald/running off with a warlord? Even spare some time for Bonnie Langford, surely the most hated companion ever? How did it feel to be a known name coming in, and having her character's nature pretty much decided by public perception of her as an actress? Finally, get some fanboys on to explain to the Muggles exactly how the Valeyard's existence is possible, "somewhere between the Doctor's 12th and 13th regeneration" (that may be a misquote). Also, take a look at the role of the Matrix in the show, get Nabil Wossname and Christopher Ryan on to do a commentary track on Mindwarp and also a short feature on being in the Mentor costumes on the shoot (if we delay the release a bit, could also get Ryan to compare and contrast the prosthetic experiences of 6th and 10th Doctor stories. Get Tony Selby on to talk about the character of Glitz (who in Mysterious Planet is much more fun than he became in later stories). Commentary track across the whole thing to include Michael Jayston, just because he has a fantastic voice ;o) Also get Russell back on, to talk about the concept of a whole series of Who with an over-arching plot-strand, which has now become standard practice. And again, get a fan-panel to assess the Trial season against what came before - and what was to follow.