You can read the NFFT 3.0 manual online (also available, in the NFFT package, are PostScript and Acrobat PDF versions of the documentation) as well as the NFFT 3.5 doxygen documentation (refman.pdf), which gives detailed information on more advanced options and parameter settings for each routine.
The most current general paper, and the one that we recommend if you wish to cite NFFT, is:
Keiner, J., Kunis, S., and Potts, D.
Using NFFT 3 - a software library for various nonequispaced fast Fourier transforms
ACM Trans. Math. Software, 36, Article 19, 1-30, 2009, (full paper
The technical report OpenMP parallelization in the NFFT software library was written by Toni Volkmer. A tutorial on NFFT was published in the 2001 in: Modern Sampling Theory: Mathematics and Applications, J.J. Benedetto and P. Ferreira (Eds.),Chapter 12, pages 249-274 with the title 'Fast Fourier transforms for nonequispaced data: A tutorial' (also in ps, pdf), by D. Potts, G. Steidl, and M. Tasche.
Detailed information of the NFFT is given by S. Kunis and D. Potts in Time and memory requirements of the Nonequispaced FFT , Sampling Theory in Signal and Image Processing 7, 77 - 100, (full paper ps, pdf).