The latest version(s) of MATLAB support NVIDIA GPU's. You can very easily run MATLAB code that performs image registration (perhaps normalized cross-correlation) on a GPU.

you can use CUDA or Brooks programming libraries which you can find now in ITK based registration methods as well and embed in your open source application.

Niftyreg, developed by the CMIC at UCLondon, has an effective GPU implementation for medical image registration. You can download the code at the following address:

http://sourceforge.net/projects/niftyreg/

and get more information there:

http://www0.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html

Phase correlation works very fast and flawlessly on GPUs.

After reading above answers, I rate Miguel Bordallo Lopez answer better than the rest.