EclipseCrossword is perhaps the fastest, easiest way to create a crossword puzzle from your own list of words. You only need to enter the answer words that you want to include in the crossword, along with each term's corresponding hint.
EclipseCrossword takes care of everything else, fitting the answer words together to create your puzzle.
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The next step is to establish the puzzle's dimensions, experimenting with different layouts to find the one that seems most attractive to you.
Finally, you'll need to choose an output format: you can print it (either just the grid with the clues or the completed grid), save it as a webpage (Javascript or Java Applet), or save it as an RTF document.
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I spent the whole afternoon trying to create a crossword puzzle. Instructions are given, but it does not explain where to write the words. Could you explain better or provide the format?