Here's a great essay from Anon136 of this forum that explains the key innovations in Nxt's unique Proof-of-Stake/Transparent Forging implementation. Definitely worth the read.
https://docs.google.com/document/d/1E_ToOMG2l1XThx6YnyXEajXaf6H1k2yjq8XkAF0ScB4/mobilebasic?pli=1I think Nxt could challenge Bitcoin in time. Some of these ideas will be hard for Bitcoin to adapt to (would require changes at the fundamental level, which might necessitate a hard fork - difficult to do when so much money is at stake). Bitcoin could possibly come up with other ways to remain competitive though. I think this year will be very interesting.
eMunie looks very interesting too. As does Zerocoin. From what I gather, Bitcoin could implement Zerocoin, but probably won't in order to cooperate with governments. It wouldn't be able to implement the Nxt or eMunie ideas without a significant rewrite though, as these have very different ways of doing things that are not based on Bitcoin.