1. Have Tom Baker Link One Of His Stories With Smith, Via Old Footage And Narration
The man's the oldest living Doctor. His reign is easily the most celebrated of the Classics. Pick an iconic story, maybe even one with a plot hole or two, plug it with Smith and have it dovetail into a new story with the same adversary. Dump Smith in via film trickery with Old Episode footage or closely matched new shots, and have Baker narrate. Fans get 4's return that they always wanted, and Baker gets to shine in ways that Little Britain has shown he's brilliant at.
2. As Above With Patrick Troughton
Smith has pretty much acknowledged that Troughton's the one Doctor he'd love to work with. Sadly, that's pretty much got to be down to video trickery and editing with Troughton long since passed on. However, his son (A Who veteran himself) capably reproduced his father for an audio adventure. Again though, rather than just 45 minutes of Forrest Gump-ery, I think this would best work as a set-up to a modern adventure.
3. Have The Doctor On The Run Again
There's a nice build in those early years, however unintentional, with the 1st Doctor often alluding that "one day" he'll go home, and then later agonizing that "he CAN'T". By the time Troughton shows up, the Doctor (his profile significantly higher now that he's do-gooding across history and space) often slinks away at story's end, seemingly nervous he might get recorded, noticed.....or caught. And he finally does get caught, by the Time Lords - the same people he "couldn't" get back to. It's hard to say WHAT could put the Doctor on the run now, but the early years of the program benefit greatly by having a silent arc based around a protagonist on the move from...something. (Plus, it made him keeping a low profile and moving on each story MUCH easier to explain.) The pay-off was not only worth it, but literally allowed a regeneration and reformatting of the show. It's hard to believe the arc-driven production team WOULDN'T love a slowburning build to something like that, AND a nod to the past.
4. Another Classic Companion Returning
Problem here is I really can't see anyone getting as great a deal as Elizabeth Sladen did as Sarah Jane Smith (Hey, she even came with K9!). And "School Reunion" really covered this territory so well that I can't help but feel it could be a retread if the return is the focus. As I mentioned, William Russell would be great to see, but the fact it only has to be a peek in sweetens the likelihood. Canon has confirmed some good companions are indeed alive and on Earth (Tegan, Ace, Jo, Jamie...) but the best bet (Brigadier Lethbridge-Stewart) passed away with Nicholas Courtney. I don't doubt it could be done and done well, but it's a long shot with the earthbound ones and any alien companion (or worse, Time Lord - Sorry Susan and fan-favourite Romana) also involve so much backstory/explanation that the chance gets even slimmer.
5. A Massive Timey-Wimey, Doctor-Fest
Oh come on, who doesn't want to see this?!?!? (Done well, I mean) It's because it's so unlikely that I've consigned it here. 7 realizes something's off when he's travelling with Captain Jack. Martha wanders off in the Tardis and nearly gets brained by Ace. 8 is convinced he's only a step ahead of the Daleks, while 10 is trying to solve the mystery that 4, K9, and 11 are desperately trying to prevent destroying them all. Meanwhile, 5 and 6 bicker jointly with Peri and ...well, you get the idea. It certainly could work (in theory) and be a "bottle" episode in the TARDIS. But I'd settle for Tennant finally meeting the Zygons when he comes back instead.....