On my alternate-history message-board, the member whose handle is Analytical Engine has been writing a Star Trek alternate timeline. Since it's posted in a members-only section of the forum, you'll need to be forum member to access it (although I've suggested he start posting it on fanfiction.net much like how I've done with "The Dragon and the Bear" to allow wider access), but it diverges from our history in the late 1980s and early 1990s with the Soviet Union reforming rather than collapsing (New Union Treaty). The Eastern Coalition forms in the aftermath of a global depression triggered by economic problems in China and the collapse of various dictatorships in the Islamic world. World War III begins in 2053 and lasts until 2057, with Khan Noonien Singh and Col. Phillip Green making their mark on history after the war--in fact, after First Contact with the Vulcans.
One of the consequences of this situation is that the sleeper ship that Khan and his loyalists flee on, the Botany Bay, is equipped with an early model warp drive rather than a slower-than-light engine. I suggested a consequence of this might be that Khan and friends find a world to settle and establish a new Augment society relatively soon after they leave Earth or they contact one of the canonical races of Star Trek before the Federation does. AE said his plan would be that they'd run out of fuel and get found by the Enterprise in a similar manner to the episode "Space Seed."
Oh well. It's his story. That being said, since the Botany Bay has a warp drive, that will definitely put it in a different location (probably significantly farther out) than when the Enterprise encountered it in canon. That means if Khan and friends try to take over the Enterprise and fail and Kirk maroons them as he does in the show, they'll be on a different planet, one that will not suffer the tribulations of Ceti Alpha V. In "Space Seed," Spock was concerned about the consequences of Kirk's actions a century down the line (i.e. during the time of Star Trek: The Next Generation). Spock was probably concerned about what the Augments might do with a virgin world and nobody to keep an eye on them, but things turned out rather differently.
I suggested to AE that a sustained Augment colonization of a different world with only the Botany Bay itself and supplies loaned from the Enterprise would end up at a probably 19th Century frontier level of development due to lack of infrastructure (although they'd have some gadgets and modern medical knowledge), but what if, say, a warp-capable alien ship were to crash there? The Augments, who'd have 22nd Century knowledge (Khan's reading the Enterprise's technical manuals and whatever Lt. Marla McGivers knows as well) even if their physical technology has regressed due to lack of infrastructure, might be talented enough to repair the ship or reverse-engineer technology from it in order to return to space. Given how their tech base would be rather primitive, whatever they could cobble together would have a distinctly steampunk or dieselpunk look to it.
AE has not gotten back to me, so I don't know what he'll do with Khan in the distant future of this timeline, but for those of you who are Star Trek fan-fiction enthusiasts, consider this a challenge. Take my scenario of Khan and friends colonizing a different world and run with it into the TNG era at least. Be sure to use steampunk space technology. Bonus points if Khan himself lives long enough to trouble Picard, Sisko, Janeway, or others from that time period.
(Hmm...an older Khan throwing down with Worf like he once did with Kirk? That'd be hilarious.)