One of my favorite applications is Jungle Disk I use it as part of my backup strategy. Since I am on a Mac and the Mac OS X generates a ton of those pesky little .DS_Store files everywhere. These files are small but do take up space and time when uploading backups to the Amazon S3 servers. Here is a simple command you can run in the terminal to prevent the generation of .DS_Store files on remote networks / file servers etc. Please note this will not prevent them from being created on your local machine.
1. Open Terminal
2. Type in the following command:
defaults write com.apple.desktopservices DSDontWriteNetworkStores true
3. Close Terminal
4. Reboot your Mac