It's basically fanon, if not canon, that Snow Crash and The Diamond Age are set in the same universe (and that Y.T. grew up to be Miss Matheson). Since "Snow Crash" is set in what is by now an alternate early 21st Century, that whole universe is separate from ours. The Big U and Zodiac, with their zainy feel, probably take place within that universe as well; their 20th Century was almost identical to ours, and it was only around the year 2000 that this universe's history began to deviate from ours.
Meanwhile, REAMDE and Seveneves chronicle a universe closer to ours (but hopefully not too close). While Hiro and Y.T. are surfing the Metaverse in their 21st Century, one universe away, Doc Dubois, President Julia, et al are preparing for the Hard Rain in their own, grimmer, 21st Century. 500 years later, humanity has evolved into different subspecies, and mostly lives off-world—in this universe. Back in the other universe, humanity still lives on Earth, and Nell is growing up with her Primer.
The events of REAMDE explain the lack of Islamic terror in Seveneves. If the end of the world was announced around the globe right now, one would expect terrorist attacks to skyrocket, as terrorists rushed to earn their 42 virgins before their time was up, and as certain nations took the opportunity to nuke Israel, the U.S., and all their other enemies. However, Abdallah Jones was so important to the entire network of Islamic terror, that in defeating him, Dodge, Zula and the rest ended up unraveling Islamic terrorism around the globe almost overnight, so by the time Doc Dubois announced Armageddon, there weren't enough terrorists left to do any significant damage.
Fans of the "Reamde" bunch, don't worry; Dodge, Zula, Olivia, Sokolov, etc. were all badass enough to be among the few survivors of humanity that managed to evade the Hard Rain. Their lives weren't exactly wonderful afterwards, but they got through.
As for where Anathem, Cryptonomicon and The Baroque Cycle fit into this, this troper hasn't read those yet. Any one of those stories might fit into one of these universes, or they might exist in some third universe.
- Anathem basically explains what you just did, since it deals with alternate universes.
