I have found a free crossword puzzle making program. It's called Across Lite. I whipped up a little one to test the program out, put in the clues and stuff, and got this result

http://www.atari2600land.com/crosswords/121.pdf

Pretty neat, huh? How I use it is I make a text file with the grid, along with unnumbered across and down clues, and it automatically numbers them and makes a normal crossword-looking grid. This is what I'll be using from now on to make crossword puzzles.