"Subversive" software is software that enables individuals to act in contrast (but not necessarily against) the status quo and to protect their rights.

Privacy

Tor - a co-operative scheme to provide anonymity for individuals by mixing traffic into a interconnected mess of peer to peer connections. Prevents traffic analysis. Reported to be used by US intelligence services to access public data sources without revealing their identity.
PGP[1] - a grass-roots public key encryption scheme capable of protecting the contents of messages.

Censorship

Freenet wikipedia: Freenet - an anonymous peer to peer network designed to enable publication of information in a manner that is difficult to censor. Reportedly used in China to protect from censorship there.