You all need to check not only the start menu of your username, but the start menu folders of "All Users" and "default user". These can be found in the documents and settings folder.
Many programs that start automatically are put in the all users folder, not just your usernames start folder.
Also many times, if you right click on the offending programs in the tray they will have an option to exit, and also to keep it from coming back again--the logitech icon that logitech mice use for easy access to the configs is one--you open it up and it has a check box that says something like show in tray--you uncheck it, and it goes away.
Very rarely will you have to do any registry editing to get rid of programs in the tray.