I am normally incredibly disorganized, and 3.5 while still my system of choice is so befuddling at times...so I actually ended up buying a laptop computer that is devoted SOLELY to DMing and game prep. I'm not sure if you'd want everything that's on it, and there's lots of redundancies, but here goes:
1) DMGenie - - this would, frankly, probably be enough even if I had NO other tools. It manages initiative, can auto roll attacks, can make Listen/Spot/Etc. checks for the Entire Party without them knowing. It accurately tracks each and every fiddly little modifier, including ENCUMBRANCE. It's not perfect, but it's close enough. It also tracks time in battle and campaign levels, has all the monsters and their stats, all the base spells, and adding feats/classes/etc is about the easiest thing ever. I even enter the adventures right into DMG, and after each fight it can divide up treasure and calculate/assign XPs.
2) The Creative Mountain SRD collection
3) Fantasy Grounds - - While for game mechanics (rolling, adding modifiers, etc.) it is next to useless compared to DMGenie, it is useful in terms of mapping, keeping track of who's where, etc. I also have Klooge, which I might tend to use in a non-face-to-face game, but for me FG seems friendlier.
4) PDF versions of many of the other books I use
With that laptop, I can actual DM anything without bringing any other books, and I don't even have to have dice, though I still tend to bring them because it just 'feels' wrong to DM and not actually roll.
5) My web site...on my web site I maintain a forum where we discuss the game logistics (who can make which dates, who wants what food, etc.) and any other topics. Also, DMGenie will export character sheets as HTML so any time a player needs to see their character all they need is a web connection. Also on my site I maintain a TiddlyWiki of all the campaign flavor stuff (gods, nations, history, notes on previous characters, major NPCs, etc).
Part of me was initially reluctant to go electronic, feeling it would take some of the connection away...but for me at least it's certainly no less distancing than a DM Screen, and the benefits in terms of keeping the game rolling are huge.