Before I begin:
The CAS/Azzie war has been simmering for a while. I consider it a full out war, however, due to what's in SoNA -- border raids, gulf attacks, stuff like that. Azzie was -extremely- pissed over the whole Denver thing (not to mention losing some of their biggest mojo).. The fact that the CAS was used as Ghostwalker's military might for the invasion is what is sending things over the top. Pueblo might get involved as well; After all, snatching up L.A. pissed Azzie to no end, not to mention "restricting" access to the Mojave. And then there's the lingering thing that Azzie's pretty much on the world's bounty list, thanks to the Big D.
A good question to ask yourself in regards to books is what you expect the tone of the game to be. Is it going to be gangers? Mafia? Smuggling? Proper Shadowrunning? Corp Work? Activisim (Overwatch and such)? Or are you going Epic level Dragons, or Epic Level Earthdawn? In my mind, those are the rankings of genres, with gangers at the bottom, and Earthdawn tie-ins at the top. Obviously sub-genres, like Lone Star/Docwagon, or Epic Level Corp intruigue, fit in there at different levels, but I think you get my point.
Sooo, analyzing what you have:
The core books are a GM's necessity. Always read the first 3 chapters of each book -- they give the background of the subject in relation to the "real world." In Cannon Companion, read the Applied Simsense rules; in M&M, read the "fluff" that proceeds the toys. As these books do not define archtypes, their layout is a bit different. Remember, however, that most of the expansion toys are meant for Smuggler genre and higher, although some may seep into Mafia games.
Lone Star obviously is the GM's toy. Kinda been replaced, rules-wise, by New Seattle... But Lone Star is a book I seriously wish to get my hands on.
Target: Matrix is a must-read in my group. It shows, better than anything, what a wired society looks like, from all angles. Check out the troll babe in the "entertainment" section.
The Neo-anarchist's books I do not have, and cannot comment on. All I know is that they are -old-.
CalFree is great for Smuggling games, and for world-hopping. It will be outdated come 2061/2, however. I found it one of the hardest books for me to finish, however -- only beaten by Shadows of the Underworld, which I wish I would've read faster.
Target: UCAS is a setting book. Use it for any genre; the politics in it have not necessarily gone away, only been modified. Boston is the most untouched area in it, truthfully.
NAN vol. 2 is completely trashed by Shadows of North America, but the NAN settings are great for Proper Running, and actually Activism stuff -- righting the wrongs in the world. In case you are wondering, NAN vol. 1 covers the "other half" of the NAN -- they just split up the book. Also note: If you get Shadows of North America, three important N.A. areas are left out. The Trans-polar Aleut is covered in detail in Target: Wastelands. Aztlan obviously has its own book. And finally, the Carib League gets the once-over from the Gingerbread Man in CyberPirates. Ahh, Miami. Always a good vacation spot.
Super Tuesday and Harlequin are both adventures. I'll leave it to you to figure out their genre and power levels (as I do not have access to either)...
SOTA: 2063 updates Fields of Fire and Corporate Security Handbook, as well as introducing a bunch of new toys. I'd tread lightly with this book, as it does reflect the crossover from 62 to 63... A year after the comet.
Blood in the Boardroom is a framework to give you an idea of runs from 58-60. The actual spelled out adventures are about Standard Run level, although it can easily spike to Corp Work, or even Epic Level corp intruigue in an instant if you wish it to. Great for GM ideas, as all the track books I own are.
Shadows of the Underworld: Mafia, Mafia, and more mafia. If you are gonna run anything with Al Pachino, read this first. Some parts are Hollywood, some are truthful, but it is a great book for low to mid level campaigns.
The Tir: Can't touch this one, but from what I have heard, it leans towards "Country work" to epic level Earthdawn. It's on my list of buys as well.
SR Companion: I want to make a special note about this core book: The back gives great suggestions for every genre possible, and is a huge GM aid. But of most import are the ganger information. This, combined with New Seattle, creates the lowest-level ganger setting.. Giving you everything you need to work in the bottom rungs of organized crime.
First Run: Another adventure, but introductory level. First adventure is ganger level, the second is Corp Work (I haven't seen any direct influence from it in the canon, therefore it isn't Epic Level Corp), and the third is Activisim/smuggling/ Standard Shadowrunning, in that general area, depending on how you look at it, and get your players into it.
RAS: The -EPITOME- of Epic Level Corp. This is not an adventure for the faint of heart. It is this game's Tomb of Elemental Evil, or the Tomb of Iuchiban, or the Underdark for that matter. It requires a lot of creativity and ruthlessness on the GM's part.. but even someone who owns RA:S doesn't necessarily know what happens. This book is also at the core of finishing the final chapter of Brainscan (as if it needed even more to make it nasty). Brainscan also holds the updates on the equipment in RA:S, to make it more compatable with 3rd. Just a small request: If you decide to throw them in here... make sure they visit the glass maze, please? The mazes are my favorite part of the SCIRE.
Athenor