I've recently re-discovered a couple of things that Windows does that have made my life a lot easier, without extra software. 

One is Win+R.  I made a folder called "c:\shortcuts" and put shortcuts to various things, such as Thunderbird and LyX, and renamed them to something easy to type.  So, when the run box comes up, I just type in the appropriate thing and it opens.  Neat.  I put a shortcut to this folder on the desktop, so that when I want to add something it is easy to find.  And, I've just discovered, you can put a shortcut to the shortcut folder itself in there, and then Win+R "shortcut" will open the folder of shortcuts!  Amazing.  How come I never knew I could do this?

The other is that you can add shortcut keys to shortcuts on the desktop, using Right Click+Properties.  So, for instance, I have a desktop shortcut to the folder that has my PhD work in it and have created a shortcut key combo of Ctrl+Alt+P, and presto!  the folder opens.  It starts faster than the QuickLaunch bar, I don't have to look at it all the time, and I don't have to navigate down multiple levels to get to it.

Since I have a tiny screen and I normally have whatever I am working on at any given time maximized, I don't particularly care about having a clean desktop.  I also find that it makes sorting things easier if I can just drag files onto the appropriate desktop shortcut and thus move them to the appropriate place, although I have also found the programs called "Folder Guide" http://www.freeware365.com/desktop/folderguide.htm and "File Targets" http://www.moonsoftware.com/download.asp handy. 

I use FARR sometimes, too, but I'm afraid that I am a little bit too dense to understand how to use it properly.   :'(

(Edited for clarity)

Apologies if this is misplaced and/or obvious.

Is it possible to combine all the AHK scripts and programs in such a way that there is only one taskbar button, and right-clicking on it would allow you to navigate to the program you want and then access the menu for that program?  Sort of like a miniature program launcher or start menu, only in the tray.