I think you're going a bit overboard there Darwin - I don't really think any program can be made to organize the start menu based off Type of program/function/name/etc. The same thing happens.. one program will always fit into another category, and that's the main point of this thread I think.. no action because of an utter need to have every thing sorted correctly and efficiently.
Basically what I propose, under All Programs.. you have a similar linux/unix categorization scheme, which goes a little some thing like this:
Multimedia OR Audio & Video
Graphics OR Graphics & Design
Games OR Entertainment OR Games & Entertainment
Internet OR Internet & Network
^--- that, imo, seems to be a good starting structure, you can then add parent categories like "System Development", "Web Development", "Programming", etc.
Now you could get carried away for example:
you're thinking "hmm, some of the items in Multimedia come under Entertainment.. some of the programs in Graphics are Tools... how should I sort those
then you're thinking "some of the Games are multiplayer games therefor they could go into Internet & Network,
"this is a nightmare, how im gonna organize this shiz?
that point is, there is none for this type of extreme and perfectionist type of categorization.