My NAS runs Linux and currently directly shares its XFS directories. Since I want to use encryption (e.g. TrueCrypt or dm-crypt/LUKS), I have the freedom of filesystem choice for the container. All clients run Windows 7, so which filesystem should I use for the shared container to have the least amount of compatibility issues? The fact that e.g. ext3 doesn't store a file creation date seems to confuse some client tools, but would using ntfs or fat32 actually fix this or is samba3 assuming a Linux filesystem anyway?
I assume you have this encrypted container on the NAS and want to share the FS inside the container via Samba. In this case, use a Linux FS like ext3/4 or XFS. That's what Samba expects and works best with, as it doesn't even know about this encryption stuff.