Creating a zip archive under linux that is windows compatible

zip -9 -y -r -q file.zip folder/

-9 Indicates the slowest compression speed (optimal compression, ignores the suffix list)
-y Store symbolic links as such in the zip archive, instead of compressing and storing the file referred to by the link
-r Travel the directory structure recursively
-q Quiet mode
folder Refers to the folder to be zipped

zip package needs to firstly be installed:

sudo apt-get install zip