You can set your Mac to not write .DS_Store files to network disks so Windows users stop complaining. Paste this command in terminal:
defaults write com.apple.desktopservices DSDontWriteNetworkStores true
Existing .DS_Store files can be removed with this Applescript:
display dialog "When you delete .DS_Store files, you will lose window size and icon arrangement for EVERY FOLDER on the target disk. Furthermore, if you had any Spotlight comments (a.k.a.Finder comments) associated with any files, they'll also be deleted"
set mountedDisk to POSIX path of (choose folder)
tell application "Terminal"
if (count of windows) is 0 then do script ""
delay 0.1
do script "find " & quoted form of mountedDisk & ¬
" -name .DS_Store -delete" in front window
end tell
I have not heard of the ._filename.xxx problem, but if you are running Apache server you can tell Autoindexing to ignore filenames starting with "._":
IndexIgnore \._.*
You configure this in the server config file or .htaccess.