Okay, so maybe you like your .DS_Store files. My machine is running as a server mostly. Those annoying .DS_Store files are always preventing me from doing stuff. Sometimes a get an error when I try to delete a folder that says "the .DS_Store file is too big and it cannot delete". Also, I do not want my windows to always be how the person before left them, so getting rid of these files helps everyone to view the folders without all the damn list views completely expanded which could slow down the Finder.

you can always edit the "RemoveDS_Store" Unix executable in /usr/bin. Change the part where there is a lonesome "/" all by itself. Add the full path to a specific directory instead of the default "/" which is the path to your startup disk. For that matter, duplicate the whole line and add as many custom paths as you want:

find /path/to/folder -name .DS_Store -delete
find /path/to/folder2 -name .DS_Store -delete
find /path/to/folder3 -name .DS_Store -delete
find /path/to/folder4 -name .DS_Store -delete