We often need to compare text files that are quite large (1-3 gigs). I am looking for compare utilities and am more focused on performance rather than aesthetics and features. We have used Beyond Compare, Ultra Compare, and Compare It in the past and they tend to error out on memory when handling these large files.
A bit more detail on your requirements might help. Writing a program to quickly compare two huge files, where all you need to know is whether they're different and where the difference starts would be very easy. The difficult bit comes when you need to re-sync and provide all the differences, but again this is not rocket science.
For performance, I'd say use C or C++, with large memory buffers. There are loads of open source examples out there, such as this