Firstly, to back up a CD properly, you'll need a ripper. On Mac, this is, or used to be, Astarte's Disc Copy, and it will read many formats, saving in Toast image format. Essential for backing up a cross-platform hybrid disc.
Secondly, Mac backup. Though invisible to the user, Mac files often have resource forks in addition to data forks. They usually contain info that's often changed, such as menu titles, graphics, etc. Makes application language translations easier, etc. Other Mac info like type/creator (the equivalent of the PC .xyz extension) is important too, but can often be recreated. Big scary thing: some Mac files become unusable when their resource forks are lost (eg. fonts).
Basically, it's safe to put "naked" (unstuffed) Mac files on a PC. It's safe to copy them around the server through a Mac. It's usually even safe to let NT move or copy those files around, since it knows about the multiple forks that Mac files use. It's not safe, though, to let Windows 98 move Mac files around, or burn them to CD. It also looks like it's not safe to let an automated, scripted copying system move "naked" files around either. Resource forks and file types are lost, and for some types of files, that's critical. Mostly it's just annoying, though fonts are killed outright.
Simple solution: putting them in a Stuffit archive will protect them in the transfer.
I've seen, in years past, a number of Mac files, without .xyz extensions, backed up by copying to a PC and burning PC ISO discs with long filenames. Macs no longer know what they are without type/creator info, and PCs don't know what they are without extensions. Plus, all the resource forks are toast, though for PSDs that usually means just Mac thumbnail previews. The files are a pain to open — almost useless. If you don't have it already, grab this safe, free Mac system extension that lets you read PC CDs with long filenames:
But a big, big rule for everyone working with any files that could possibly be opened by someone on a Mac, ever, is to keep within 31 characters for file names. Over that, names become meaningless as they are translated into 8.3 DOS format (AFTERM~1.doc). Hopefully this will go away with Mac OS X later this year.