While RSA and other widely-used cryptographic algorithms are based on the difficulty of integer factorization (which is not known to be NP-complete), there are some public key cryptography algorithms based on NP-complete problems too. A google search for "public key" and "np-complete" will reveal some of them.
(I incorrectly said before that quantum computers would speed up NP-complete problems, but this is not true. I stand corrected.)
