Add one or more folders to .zip archive

To add single directory (with all files and sub-directories) simply execute:

zip -r zip_file_name.zip name_of_your_directory

To add all contents of current directory (again, recursively) call instead:

zip -r zip_file_name.zip *

While to add two or more directories (but not all) in current directory — list them:

zip -r zip_file_name.zip directory_a directory_b directory_c

Call just zip to see all switches, options etc.