Okay so it's probably not THAT Doctor, but in another bit of news from io9, it seems
Twin Peaks veteran Kyle MacLachlan will be showing up in ep 2 of the second season of Marvel's
Agents Of S.H.I.E.L.D. as some kind of practitioner of medicine/science..and it's unlikely to be a in a scene with Coulson looking for a prescription for the flu. They also report that Glenn Talbot (Adrian Pasdar) will be back to give the team headaches in the season premiere.
"A source tells io9 that the premiere will see the return of Adrian Pasdar's Glenn Talbot, and that the second episode will guest star Kyle MacLachlan as "The Doctor."
To be fair though, this show does feature a great many nonspecific doctors, scientists etc so it may just be a character written for this one episode -- but, it could also just as easily be an established character from the comics and MacLachlan will return for future appearances. Either way, he's a fine actor so it'll be interesting to see which role he ultimately ends up in.
UPDATE: TV Line report that MacLachlan will actually be playing Skye's father!