It is odd since EFF's Tor continues in development. Freenet has been having some difficulty with the magnitude of the v.0.7 changes though its progressing.
Tor is like an anonymous proxy, except the proxy owners don't know who or what you are looking at, and traffic between the proxies and the clients is encrypted. Its like a P2P proxy. Tor requires users to "donate" tor servers by allowing their computer to relay traffic for other users.
Freenet is an anonymous P2P network. Its similar to crossing eMule with HTTP. Where Tor can be a proxy for any TCP protocol (mainly used for HTTP), Freenet has it's own protocol and is a seperate network from HTTP. Freenet is similar to BitTorrent in that there is a "tit-for-tat" system where you must allow upload in order to download - by running freenet, you automatically donate your computer's resources to help anonymize others.
Theoretically you could use Freenet and Tor together as they tackle different anonymity issues, but going through one is slow enough.