I am the novice to JWT token usage, while reading came to know from jwt.io that there are six versions with different types of binaries are available as below.
Can anyone please explain to me what is the broad difference between them, except java version support.
A JWT can be cryptographically signed (making it a JWS) or encrypted (making it a JWE):
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Take your pick based on the features supported by each implementation. As mentioned in the comments, JJWT and Nimbus JOSE + JWT seem to be the most widely used libraries for JWT in Java.
See the documentation for details on usage and supported features of both libraries: