I've been using various methods for online organization of my game, and pondering the ideal solution for a while now.
I've pretty much come to the conclusion that I may need to write a GMS (Game Management System) myself, as I seem to want it to do most everything for me. I thought a web-based, php system would be nice, with the following features:
World management (complete world stats, marked either for DM or Player view, as well as special groups - so your northern barbarian would have access to the northern customs and geography sections, etc; map indexing - including virtual lat/long coded in so you could place a city description in the world guide and just link its location, etc; Sections for different cultures, races, areas, cities, religion - down to as specific detail as you cared for, with customizable entry fields, etc..)
Feats, Spells, Equipment, Monsters etc - data collections for each, with an appropriate 'ok for play in this campaign' setting, so it would only show the appropriate equipment for a Dark Sun campaign, for instance. Each would be customizable as well as having the 'standard' fields (need a 'description' field for a specific sword? no probl, just add it in).
Character Tracker - probably the same system for NPC and PC, with different output views for the DM (just want a stat block? check this box..) This would track character xp (so the player would always know what their total is (my players are so bad about not putting this down right.. I swear..) - and could even help calculate it by CR and EL if you put those in. It would be easy to update your character between sessions, then it would auto calc your encumbrance (if desired) and all the other bookkeeping crud that players don't want to deal with (for the most part). It would hold a wizard's spellbook and keep track of pages as well.
Integrated messaging for players to leave notes for the GM, and vice versa - it would email you when you had new messages waiting. The DM could configure it to allow players to PM (basically) each other as well if he liked.
Multiple campaign options - the DM could create a campaign, assign which data sets (books/sources) he wants available (with indivicual exceptions if he wanted (all of the FR stuff, but no tattoo magic, for instance). The players would create a character, tie it to that campaign, and then would automatically be given the correct options to choose from when picking a feat/spell/equipment.
I would use it for tabletop play, but I could see adding a chat module or somesuch for online play as well, with a dice roller and a database link to browse your character and/or world info at the same time. Wouldn't necessarily need to have this integrated though.
I also like the idea of making a table of 'keywords' that would be processed and linked dynamically - so that when the php processor sees 'Great Cleave' written, it knows that is a feat and links it to the great cleave description. That could get annoying, so there would of course be an option to turn that off or customize what categories of keywords it links.
I have some notes somewhere, but that's the gist of it. The beauty of the whole thing being online is that I could use a tablet PC or whatever at game if needed, or print off stuff if that's how I wanted to go. I really like the idea of being able to add a city idea, or a new monster from wherever, when the idea hits me (assuming I'm near a computer, which I pretty much always am). Player forgot his character sheet (or didnt' show and someone else has to play him)? - zip online and print the absolute latest copy from your DM account. Forgot your printed notes? Just do them again! Want to add a new city that you made up on the fly when your players' teleport went awry? Take a 5 minute bathroom break and plop that sucker in.
That, to me, would be the greatest. Kinda like what I hoped E-tools would be in the beginning, but fully networked and online. It combines a lot of other functions into one, and gears them specifically for RPGing. I have yet to see a product like this, other than 'you could take this CMS, add a mod here, tweak that there..." - and it still doesn't necessarily do it quite the way I had in mind.
I did some work on this, actually - getting the spell data module mostly built, but then the 3.5 revision and a severe lack of time kinda punted it back into the land of 'pipe dreams'. I hadn't really planned it well from the point of view of integrating it with the other modules though, so it lacked session support and such. If I did this now, I'd do a framework, then each individual module to make sure it worked right. It is certainly a feasible project, but quite a lot of work (including the huge data entry chore). Would be worth it if I had the time to do it though.
If anyone has something out there that seems similar - by all means let me know. I certainly haven't seen anything quite like this yet though.