Ok, books I'd like to see in no particular order:
Stuff - A 2 e version of the Zocolo book, fleshed out. There's a galaxy of gadgets, trinkets and artifacts out there, and a book to help flesh all that out would be handy. Anything from a low-watt Narn lightbulb to Technomage-crafted weaponry, from self-refrigerating Centauri goblets to Shadow artifacts. Also this would be a good place for trader and crafter prestige classes.
Mindwalkers - JMS has said that he's got an outline of G'Quon's crusade, and the Mindwalker's last battles. Even without access to those notes, this would make an interesting adventure. It'd also give the PCs a chance to do something different, as well as be a part of history. This could either be a short game, like Cold Equations detailing the final battle, or a lengthy campaign involving everything from the Shadows' arrival to the final climactic push.
Megacorps - A book detailing the megacorps. I don't know if it's been done before (Merchants, Traders and Raiders, maybe?) but a book that takes a look at them in broad strokes would be very helpful. How did they get so much money? How diversified are they, and what else are they into? What are some common practices they use for circumventing local law in whatever system they are operating in? How large a hand do they have in EarthGov and elsewhere? In addition to this, alien megacorps could be examined (the Brakhiri, for a start).
Telepathy - A book detailing telepathy across the galaxy. Not just Psi Corp (though Psi Corp does need to be included in a 2e book), but how each race deals with telepaths. Race specific telepathy powers (such as a Brakhiri's advanced surface scan to use while bargaining, or a Minbari Warrior's battlemind, or what have you). Race specific telepath prestige classes, and non-Psi Corp prestige classes, not to mention low-P level prestige classes. The Telepath War and its impact on Earth could also go here.
Hyperspace - This one seems out there (but then I thought playable Technomages or God help us playable Vorlons were out there too), but a book on hyperspace would be interesting. If the Well of Forever ep. of Crusade is any indication, hyperspace has a lot of room for just about anything. Ghost ships, temples, graveyards, ancient treasure vaults, monsters, Psi Corp motherships, not even to mention Vorlon pockets and Shadow vessels. This would also be a good place to include travel times based on engine size/speed, complications that could arise on even a mundane journey, off-the-beacon travel (whether it's luck, following a Shadow ship, or some alien tech), and any number of locations for weridness to happen. Even off-the-beacon jumpgates (damaged, forgotten or deliberately hidden?), planets or even systems would fit in this book.
Outside the Timeline - 2e is timeline neutral, but a book that fleshes out both before (Dilgar War, In the Beginning and the time between the Battle of the Line and B5 going online) and after (Telepath War as well as Call to Arms/Crusade) would be helpful.
Advanced Tech/Black Projects - FuryMaster mentioned this and I want to second it. A book that talks about what each race is currently developing as its cutting edge tech, as well as black projects from each race associated with the tech race would be a very fertile ground for plot hooks. Every project would have numerous angles for a GM, and would also help to flesh out what each race considers top priority and what they're missing out on.
ISN - I will also second Mongoose Gar's ISN book. I'd LOVE a book that fleshed out ISN's operations, as well as material to allow my PCs to work for someone other than a corp or a government. (Not that they can't already, but a journalist is still a great PC idea...)
Vicker - This isn't a book, but I think a Vicker prestige class included somewhere would be cool. And it seems like a cyber mod that doesn't require Vorlon intervention, so it might even be possible. Photographic memory can be a pain for a GM, but the idea of a prestige class with Investigate and Notice as prerequisites makes me happy. Class feats would probably include various things one could record (light, sound, thoughts, etc), recording times w/o channging data crystals, and other goodies.
