Teased of clients asking why you have that hidden .DS_Store in folder? Here is a quick tip on getting rid of when compressing a folder. Anyways, you're not afraid of terminal, are you?
zip -r name.zip name -x "*.DS_Store"
If you need to remove multiple files you can do this.
zip -r name.zip name -x "*.DS_Store" -x "*.svn"
That's it. Dead simple.