I use a hodge podge:
FreeCommander for opening media files with an info app, subtitle utility, player, skwire's PlayTime etc. since I have those tools in the toolbar configured to open the selected file.
In Vista I use QuickLaunch.
I use my own ReOpen mostly to reopen folders. If I type a substring that's not in the list I hit ^c and that brings up Everything Search and enters the substring. A middle mouse click on the desktop brings up the pop-up window. No taking my hand off the mouse unless I want to type a search string.
For launching with highlighted text such as opening another browser I use my own Selector.
I made 6 categories of folders for application shortcuts. I had these in a folder on the desktop, but I moved it to Documents so that it's hidden and put the 6 categories on RocketDock. Not a single desktop icon now. I don't care if AutoArrange is on or off anymore!
7stacks. Just gives more room on the QuickLaunch or Taskbar. The apps I use most I put in categories such as Internet, Editors, Media(such as Imgburn and encoding apps), File Handling such as FreeCommander, my own Hotkey utilities. An ordinary folder could do the same but the pop-up glass panel looks cool and it's free so why not?
The Windows Start Menu is the last resort. Usually to look for a Readme file or an uninstall that may not be in the Programs and Features list.