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Deluge
Very nice, full-featured BitTorrent client.

Frostwire
P2P file sharing application with BitTorrent support. Better than LimeWire — and free.

GNUnet
GNUnet is a framework for secure peer-to-peer (P2P) networking that does not use any centralized or otherwise trusted services. A first service implemented on top of the networking layer allows anonymous censorship-resistant file-sharing. Anonymity is provided by making messages originating from a peer indistinguishable from messages that the peer is routing. All peers act as routers and use link-encrypted connections with stable bandwidth utilization to communicate with each other. GNUnet uses a simple, excess-based economic model to allocate resources. Peers in GNUnet monitor each others behaviour with respect to resource usage; peers that contribute to the network are rewarded with better service.

GNUnet is part of the GNU project.

aMule
P2P file sharing client.

Transmission
Transmission is a BitTorrent client designed from the ground up to balance power with simplicity. Its initial preferences are set so that things just work, while advanced features like watch directories, bad peer blocking, and the web interface can be configured with just a few clicks.