Do you see all sorts of ".ds_store" and "._" files lying around on your external drive when you plug it into a Windows machine? Like this MacOSXHints reader, did you browse your company's network with your Mac, leaving a trail of ._ds_store and .Trash files in your wake? If you're nodding your head right now, I think I've found the solution for you: BlueHarvest, a preference pane that lets you manage and easily clean up these various kinds of Mac OS X-specific hidden files.
BlueHarvest allows you to specify where these hidden files are created, offering different drive categories (startup disk, Servers, non-HFS disks, etc.) and allowing you to specify volumes and folders to leave alone. It even has a slick preference tab for drag and drop cleaning of .DS_Store files and resource forks from disks and directories.
I've been playing with this for a couple days now and I have to say: it's pretty handy. I have a little flash drive I use for school and a SonyEricsson phone that I can mount on my Mac, both of which I can *finally* say are truly devoid of pesky hidden files. BlueHarvest works on 10.3.9 and 10.4.x, offers a 30 day trial and costs a mere $10 - small price to pay to regain your hidden file sanity.