I've heard a number of people praise the Greiner-Hormann algorithm for clipping arbitrary polygons. They say it has a certain conceptual simplicity and elegance.
@jasondavies is utilizing Greiner-Hormann for D3's polygon clipping operations (2D and spherical). He recently gave a demo of boolean operations on polygons based on as-of-yet unreleased work here.
His earlier clipping demos can be found here and here.
@w8r has a nice, clean implementation of the algorithm for 2D clipping operations with no dependencies. He provides an adapter for clipping polygon regions defin