Compress without .DS_Store and __MACOSX
You can use zip command in Terminal to zip the files without the .DS_Store, __MACOSX and other .* files.

Open Terminal (search for terminal in spotlight)
Navigate to the folder you want to zip using the cd command
Paste this:
zip -r dir.zip . -x &quot;.*&quot; -x &quot;__MACOSX&quot;



Example
Let's say you have a folder on your desktop called Folder with stuff to zip. 
Open terminal and write following commands: 


cd Desktop/Folder



zip -r dir.zip . -x &quot;.*&quot; -x &quot;__MACOSX&quot;



Now you have a file called dir.zip without __MACOSX and .* files in the folder Folder on your desktop.