I need to programatically encrypt a directory of files, like in a .zip or whatever.  Preferably password protected obviously.
How can I accomplish this, and WHAT IS the BEST  encryption way to do it, if applicable?
Programming language doesn't matter.  I am dictioned in all syntax.
How can I accomplish this, and WHAT IS
  the BEST encryption way to do it, if
  applicable?


tar and gzip the directory. 
Generate a random bit stream of equal size to the file
Run bitwise XOR on the streams

Only truly secure method is a truly random one time pad.
Best way to encrypt a directory of files?