First of all, my advice is you should get rid of the habit of accumulating all the shiny objects out there. They will slow you down or keep you away from you road to success in this online endeavor.
If you still want to organize your stuff, I suggest to classify them into category. For example: course, tool, software, websites, graphic,...and make each cat a folder and each sub folder.
Hope this helps.
"We Will Become What We Think About"