I need to post this somewhere on the internet so that I'll be able to find it again, and other people will be able to find it.
10.5 institutes a new feature called File Quarantine. It sets a HFS+ attribute to files that were "downloaded from the internet", effectively locking them from certain file operations until cleared in the GUI. When double-clicked, these files will give some warning about executing them. Fine.
When files are transferred to an OS X Samba share from Windows 2008 (and probably Windows 2003 (Win2008 & Win2003) and probably any other system), the Quarantine attribute is set. You can see this by in a terminal entering "ls -all" in the folder, and noting the "@" at symbol in the permissions for the new files. These files are "Quarantined". Fine.
When trying to copy these files from the share to another machine, Windows 2003 will give the error "Cannot copy <filename>: Cannot read from source file or disk". Windows 2008 will give the error "Invalid File Handle". The file is not corrupted in any way despite these errors being associated with disk corruption and corrupted data (specifically a WHS drive corruption issue). The file is simply "Quarantined", which Samba is respecting (or is affected by), and Windows is simply freaking out. This is not a Windows issue despite looking like one, and the Apple Quarantine feature explains a few Windows people freaking out lately.
I've been searching, but there appears to be no way to disable Apple File Quarantine directly. One option is to set more "safe" file extensions or MIME types, another is to run an apple/shell script that unsets the quarantine attributes recursively over every drive. The apple UNIX application in question is xattr, which has no man page. The command would be "xattr -d com.apple.quarantine thefilenamehere", but here that gives the error "No such xattr: com.apple.quarantine", and there appears to be no fix for this.
If this post in the wrong place, please move it instead of deleting it, since I want people searching for the information to be able to find it. I'd also like to thank Apple for emulating Microsoft's quagmire of various and unhelpful security "features".