Aliases
Rather than fill up your file system with links you might want to just make aliases to these directories, and store them in your ~/.bashrc
file. You can then just type things like this:
alias edxPhy2013="cd ~/Documents/Courses/EDX/physics2013/"
alias cglProj-v-2.13="cd ~/Documents/Company/OpenGL/Proj/..."
alias flAndrProj-v-1.1="cd ~/Documents/Freelance/Android/Proj/..."
Now when you login, these will just work from any shell that makes use of the ~/.bashrc
file.
Directory Bookmarking Tools
Take a look at this Q & A titled: Quick directory navigation in the terminal. Tools such as autojump or xd - eXtra fast Directory changer, can be used as well to "bookmark" frequently used directories so that you can easily change to them without having to type long paths.