I know that NTFS supports encryption but otherwise is closed source. Likewise, I am aware of add-ins such as truecrypt but I am interested in encryption being built-in vs being bolted on.
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No.
There's Bitlocker, but it's implementation is closed source. Everything else not manufactured by Microsoft will, by definition, be "bolted on". Microsoft doesn't provide any open source filesystems in their OSes, AFAIK.
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Keep in mind that encryption is often not done at the filesystem level. It's done at the block level, where sectors are actually read/written to disk. This allows one to use any filesystem with the encryption, as the filesystem sits on top of the encryption layer.
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Any specific use cases?
TrueCrypt supports full volume encryption, with a boot password. I have been unable to confirm this, but I believe that BitLocker also requires a password at boot. TrueCrypt is the only option I've been able to find, and it is relatively mature. Full disk encryption with TrueCrypt would be transparent - I'm not sure what you mean by "bolted-on", but I assume you mean not having to mount an encrypted volume each time you log in.
Edit: Unfortunately there is no version of FUSE for Windows. There are the Dokan libraries, but they're not widely used AFAIK.
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Personally, I use TrueCrypt, but PGP is excellent too.
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