XWord is a crossword puzzle program designed to be highly configurable. It supports a variety of formats: puz, xpf, jpz, and ipuz. Includes support for rebus puzzles, "trick" puzzles, diagramless puzzles, scrambled/locked puzzles, and a timer.
Very good software. It would be even better, if you add Python scripting.
This is hands-down the best crossword-solving software out there. We just need a Mac version now! (hint)
Very much improved over the other clients out there like Crossword Solver and Across Lite. Polished, and very customizable interface. Lots of extra add-on tools like clue search cross-reference jump, and best of all a puzzle downloader. 5 stars.