You're not alone in thinking that the DM has a lot of opportunity to speed up their job and make everyone happier. That's why a number of commercial and freeware game assistants have popped up over the years.
Because of licencing, it's very difficult for a home-brew developer to whip up a complete "every book referenced" assistant, but a few come close.
Virtual tabletops and map software are abundant, and you can find a lot of information about the free and not-so-free versions here. Even if you don't plan on using them for in-game, they can be invaluable tracking tools for a GM's arsenal. These often include virtual dice rollers, logs, and other excellent tools like you mentioned on your wishlist.
Spellgenhas nearly every spell and psionic ability in all of DnD, including the stuff that Wizards of the Coast puts out in nearly every non-core rule-book. Also allows you to enter in your own spells, powers and special abilities. FREEWARE, and maintained by several good peoples, including one of my buddies Alex.
Part Virtual Tabletop, part RPG Toolset, some of the best I've seen can be located at RP Tools, including one of the nicer map softwares, initiative trackers and character statistic trackers I've seen yet. Some of the programs are a bit clunky but most are the high end of elegant.
One of the reasons nobody has come up with a "Definitive RPG helper" is because the gaming systems are many and keep changing. Even a "D20" or a "GURPS" helper has to make an insane amount of allowances for additional rules, options and ideas.
The GURPS Character Assistant is amazing for both game masters and players, but again, it's specifically built and designed by Jackson Games, so they have full control over the content. Even though it works nearly perfectly, it's still a massive undertaking unless you know the GURPS system inside and out to build anything but the simplest character. Also, it costs 14 bux.
Overall, what I've found that works the best is still pencil-and-paper. I have used a laptop to assist often, but in the end, I find I can get by simply by having flexibility. Every time I've tried to generate maps, or update character listings, it ended up taking more time than it was worth. I may try again as my new campaign is looking to be a LOT larger than normal but even then, when we actually sit down to game, I don't want to be relying on a tool that takes any more time to load or work than a spreadsheet or HTML-linked SRD. Like anything else in true Role Playing, though, it really depends on how much effort you put into it, and you can make even just one or two of these freeware tools save you TONS of time if you make the effort to learn them.