It is very important to have your Eclipse IDE as optimized as possible. It is essential for me to see all "hidden" files and directories such as .gitmodules, .project, .classpath, but I do not want to see .DS_store as it is useless to me.
In your Eclipse > Package Explorer > click a small triangle drop-down > Filters..
Add ".DS_store" and any other file patterns comma separated.
Press OK to save.