TrueCrypt is no longer an active project for reasons that are unknown. The Code of TC has been analyzed not long ago and as far as I know the detected issues are not too serious at the moment and it's probably more secure than data that is only secured by a Windows-Login
However
VeryCrypt is an alternative that is still an active project. I don't know if VeraCrypt can be used with a Yubikey too, but it would be nice. There are many more options for file encryption (GnuPG, PGP, ...) that might do the job too.