zip -r archive.zip dir_to_zip


from man zip

-r  
   --recurse-paths
          Travel the directory structure recursively; for example:

                 zip -r foo.zip foo

          or more concisely

                 zip -r foo foo

In  this  case, all  the  files and directories in foo are saved in a zip archive
named foo.zip,including files with names starting with ".", since  the  recursion
does not use the shell's file-name substitution mechanism...


Even if it functions well I would like to propose you 7z(http://www.7-zip.org/).

  7za a directory.7z  directory


It has a better compression and it is opensource, GNU LGPL license, freely available for windows,linux,BSD... 

BTW it creates/opens 7z, XZ, BZIP2, GZIP, TAR, ZIP and WIM,
and open unpack only: ARJ, CAB, CHM, CPIO, CramFS, DEB, DMG, FAT, HFS, ISO, LZH, LZMA, MBR, MSI, NSIS, NTFS, RAR, RPM, SquashFS, UDF, VHD, WIM, XAR and Z. 

[They should pay me for advertisement :-)]