Are there any implementations for zero-knowledge proofs of NP-complete problems?
The answer is yes, check the following paper:

SNARKs for C: Verifying Program Executions Succinctly and in Zero Knowledge
Eli Ben-Sasson and Alessandro Chiesa and Daniel Genkin and Eran Tromer and Madars Virza
http://eprint.iacr.org/2013/507
(also published at Crypto 2013)