You should have your Start Menu organized.  You should have major categories such as "Audio", "Graphics", "Games", etc, for all the programs you use.  The only items in the "Programs" area should be the stock Windows stuff.
 

WinXP:

To set up the Start Menu:

• First, click on the Task Bar with the right mouse button, open 'Properties', click on the 'Start Menu' tab, 'Classic Start Menu', 'Customize' button.  Check "Show small icons" and uncheck "Use personalized".  OK, OK.
   
• Click on the "Start" button with the right mouse button, select "Open".  This is where your main folders go.  Go ahead and make whatever categories you need.
   
• Now open the "Programs" folder and move all of the icons to their proper new folder.  Just move the actual programs, not the folders they're in with all the accompanying garbage.  Remember, you're not deleting any actual files, these are all just shortcut icons.
   
• Open 'Accessories' and move any icons you want, like Notepad, Wordpad, Calculator, Paint, etc, to their new folders.
   
  Note that there's another folder full of shortcut icons, which is why you're not seeing all of your programs.  We're going to get this area tidied up first, then we'll tackle the second one.
   
• Whittle all of your icon names down to just the program name, drop the manufacturer's name and version number, keep things clean.

You can also put things like text files in the Start Menu.  Just grab the icon, d-r-a-g it over to the Start Menu and drop it in.

Okay, once everything's all tidied up, it's time to go fetch the second folder:

• Open C Drive, "Documents and Settings", 'All Users', 'Start Menu'.  That 'Programs' folder is the second folder.  When a program is installed, it often asks if it should be available to 'that user only' or 'everybody'.  If you select 'everybody', the icon goes in this folder.  It's also usually the default folder if the install program doesn't ask.
   
• Click on the 'Programs' folder with the right mouse button and make a shortcut icon.  Name it something like "Start 2" or "Other Start", to differentiate it between the first 'Programs' folder.
   
• Speaking of which, open the first 'Programs' folder.  Drag the 'Start 2' icon to it.  That'll give you quick access to both folders.
   
• Open the 'Start 2' folder and get everything taken care of.

In the future, after you install a program, it'll just be a quick matter of opening the first folder via the Start Menu button, finding the new program icon and moving it to the proper folder.  Won't take but a sec.
 

Vista:

To set up the Start Menu:

• First, click on the Task Bar with the right mouse button, open 'Properties', click on the 'Start Menu' tab, 'Classic Start Menu', 'Customize' button.  Check "Show small icons" and uncheck "Use personalized".  OK, OK.
   
• Click on the "Start" button with the right mouse button, select "Open".  This is where your main folders go.  Go ahead and make whatever categories you need.
   
• Now open the "Programs" folder and move all of the icons to their proper new folder.  Just move the actual programs, not the folders they're in with all the accompanying garbage.  Remember, you're not deleting any actual files, these are all just shortcut icons.
   
• Open 'Accessories' and move any icons you want, like Notepad, Wordpad, Calculator, Paint, etc, to their new folders.
   
  Note that there's another folder full of shortcut icons, which is why you're not seeing all of the programs on the system (both Windows' and yours).  We're going to get this area tidied up first, then we'll tackle the second folder.
   
• Whittle all of your icon names down to just the program name, drop the manufacturer's name and version number, keep things clean.

You can also put things like text files in the Start Menu.  Just grab the icon, d-r-a-g it over to the Start Menu and drop it in.

Okay, once everything's all tidied up, it's time to go fetch the second folder:

• Open C Drive, "ProgramData".  It's a 'hidden' folder, so if you don't see it go to Control Panel, 'Folder Options', 'View' tab, check "Show hidden files."
   
  In the 'ProgramData' folder, open 'Microsoft', 'Windows', 'Start Menu'.  You'll see our second 'Programs' folder and a few misc icons.  Delete the misc icons unless you use them.  (if you do, move them into the 'Programs' folder and put them where they properly go later)
   
• Click on the 'Programs' folder with the right mouse button and make a shortcut icon.  Name it something like "Start 2" or "Other Start", to differentiate it between the first 'Programs' folder.
   
• Speaking of which, open the first 'Programs' folder.  Drag the 'Start 2' icon to it.  That'll give you quick access to both folders.
   
• Open the 'Start 2' folder and get everything taken care of.

In the future, after you install a program, it'll just be a quick matter of opening the first folder via the Start Menu button, finding the new program icon and moving it to the proper folder.  Won't take but a sec.
 

Win7:

To set up the Start Menu:

• Open C Drive, "ProgramData".  It's a 'hidden' folder, so if you don't see it go to Control Panel, 'Folder Options', 'View' tab, check "Show hidden files."
   
  In the 'ProgramData' folder, open 'Microsoft', 'Windows'.  Make a shortcut icon of the 'Start Menu' icon.  This is our main Start Menu folder.  There's also a second one we'll have to deal with.  Place the shortcut icon someplace permanent and name it something like "Start1".  Grab it with the mouse and d-r-a-g it over to the Start Menu for future reference.
   
• Open the 'Start Menu' folder.  Go ahead and make your main folders.  I use:
   
  Audio — Audio-related programs
  DTP — Desktop publishing, word processing, dictionary
  Games — I'd be lost without Duke Nukem guiding my way
  Graphics — Image studios and such
  Net — Internet-related programs
  Tools — Misc tools with 4 sub-folders
  Video — Video-related tools
   
  Move any loose icons to the proper folders, delete anything else.  By the time the dust settles, you should only see the 'Programs' icon and the ones you've created.
   
• In the 'Start Menu' folder, open the 'Programs' folder.  Make it just one row wide and pull it down to the bottom of the screen, then push the 'Start Menu' folder up to the top so you can drag the appropriate icons to your custom folders.  Most folders tend to open on the upper part of the screen, so this'll keep the category folders handy for easy dragging.
   
  Go through the program folders and move just the program icons to their proper folders.  Rename them to just the program name.  Take care of everything except 'Accessories' and 'Administrative Tools'.
   
• Move the 'Administrative Tools' icon to the 'Accessories' folder.
   
  By the time you're finished, the only icon in the 'Programs' folder should be 'Accessories'.
   
• Now we have to get the second 'Programs' folder taken care of.  Open C Drive, 'Users', '(user name)', 'AppData', 'Roaming', 'Microsoft', 'Windows', 'Start Menu'.
   
  They weren't trying to make this easy, were they?
   
• Open the 'Start Menu' folder and make a shortcut icon of the 'Programs' folder.  Put it next to the first one, naming this something like 'Start2'.
   
• Again, push the 'Start2' folder down to the bottom of the screen and open the 'Start1' folder at the top.  Go through the entire folder as before, moving just the program icons to their new homes and renaming them to just the program.  Leave the 'Accessories' and 'Administrative Tools' folder alone.
   
  Open the 'Administrative Tools' folder.  If it's empty, just delete it.  Otherwise, move it to the 'Accessories' folder.
   
  Now drag the 'Accessories' folder over to the 'Programs' folder in the 'Start1' folder and drop it in.  It will note that there's already an 'Accessories' folder inside.  Tell it to overwrite it.  The 'Start2' folder should now be empty.

In the future, after you install a program, it'll just be a quick matter of opening the 'Start1' folder, then finding the new icon in either that folder's 'Programs' folder or in the 'Start2' folder.  Rename the icon to just the program name, move to its new home, delete everything else.