What free tools for managing java keystores and security certificates available around

Try portecle. At least, it has a GUI :-)

EDIT (sept. 2020) Keystore Explorer is in fact more feature complete and more user-friendly.

One more alternative is openssl.

From self experience:
keytool. It worth to keep in mind that it handles only public keys. Do not waste few days to figure it out ;)
Portacle is able to manage private keys. Are there any advantages to use command line tool if you are not trying to use it in some automation scripts than to use user friendly GUI tool?
OpenSSL appeared to be most feature rich as for me. It is able to handle not simplest situation like to create CA and sign some self signed sertificate, i.e. to create sertification chain. Creating Certificate Authorities and self-signed SSL certificates

keytool

http://download.oracle.com/javase/6/docs/technotes/tools/solaris/keytool.html