Things I hate in relation to software:

1. Application Data
   This is a folder that is commonly mis-used, It should store data related to the application (For example: user preferences) and is not a location where you can save files from the application.
   
2. My Documents
   This is a default location where user files should be stored. Not Application data, program files ect.
   
3. Creating Folder in My Documents
   There is no need to create folders that may never be used, wait till the folder is actually needed before creating saving in it, and only store files in it, not the user preferences/application data
   
4. Start Menu
   A. Give your entries a meaning full name and don't keep making multiple folders for different versions (For Example: Application Y 10.2 and later create Application Y 11) when they point to the same files
   B. Have multiple folders for the same application (For Example: a folder for the tools and one for the main application).
   C. Sort/Organize your applications into sub folders by some nice scheme instead of having them just littering the list. For example, I like application sorted by company for neatness. For example:
   

   ┌Microsoft┐
   │         ├Virtual PC
   │         ├Office┐
   │         │      ├Word
   │         │      ├Excel
   │         │      ├Magic Tools Folder
   │         │      └Ect
   │         ├Visio Modeler
   │         ├Other Application Suite 1┐
   │         │                         ├ Program One
   │         │                         └ Program Two
   │         └Other Application Suite 2
   └Autodesk┐
           ├Autocad
           ├Inventor
           └Revit

   
   

5. Place and Name your folders properly
   A. Don't just create your folders in random spots, For example create application data folders in the App Data folder not the main profile folder (Looking at you Dia/G.I.M.P.)
   B. When they are placed properly, give them a meaning full name (For example someone looking in my App Data folder might not know that .purple belongs to Pidgin)