^I know that one. I was wondering more about the source for all those other numbers and who's responsible for coming up with them.
I know some of the numbers come from that Alan Moore Captain Britain series, others from the Exiles comics and various other reality hopping hero stories like Howard the Duck's appearance in Marvel Zombies. Most though, come from various "Official Handbook to the Marvel Universe" issues. This wikipedia page list the sources for most of the number designations. I don't know that there is an official system for it (the people in charge, Joe Quesada and Tom Brevoort are not actually fans of the system, feeling it's far too derivative of DC and an era of DC they didn't like), but most of the numbers seem to have a basis in the date they were created.
I found a good list of the Marvel timeline numbers for just the TV and movie tie-ins here: http://www.uncannyxmen.net/forum/forum_posts.asp?TID=10994 Interesting that they don't count the '90s syndicated Marvel Fantastic Four, Iron Man, and Hulk shows in the same reality as the FOX Spider-Man & X-Men shows, even though a few characters and actors crossed over between them (Robert Hays as Iron Man and James Avery as War Machine guested on Spider-Man, and at least one actor from the syndicated FF reprised their role on SpM's "Secret Wars," though the rest of the FF and Doom were recast). It was always a little ambiguous whether those two sets of shows were in the same universe or not; I can't think of any blatant contradictions. (However, those three syndicated shows don't entirely fit together with each other; the Hulk episode in IM depicts a version of Hulk's origin that's completely incompatible with the later Hulk show, although the Hulk episode of FF from the same year had a sequel of sorts in the Hulk show. But I'm pretty sure there were crossovers between the paired IM & FF shows that linked them in a shared universe.) Anyway, this is off-topic. I guess the point is, there are other franchises where different interpretations are fully embraced as separate realities, so there's certainly room for applying that point of view to Trek tie-ins. Personally I only count some books and comics as alternate timelines -- things that could plausibly be divergent histories of the same basic universe with the same overall history and physics and evolution and geography and so forth. (I have two main alternate timelines that I put those books and comics into, one for the 23rd century and a smaller one for the 24th century, because the first one would've diverged too far by the TNG era for the others to fit in.) The rest, I just count as different fictional continuities. But other fans can and do see things differently. There's a variety of options.
That actually sounds pretty cool. A Federation that, quite literally, had to pick up it's pieces and start all over with new faces? Imagine the amazing stories that would've come out of it.