Just spent the last 2 hours online, preparing a crossword for the Mac User Group's monthly magazine. It's done via Crosswordlabs.com. In their web app, enter the clue, space, then the answer and go to the next line. When you have enough clues, save a passwrd so you can get to the answers later. Next, hit the Generate button. A crossword grid with your clues is displayed. Keep hitting the Regenerate button until a suitable pattern is shown.
Next, I saved the URL of the page as a bookmark and exported both the clues and the answers as PDFs.
The Clues is a blank grid, so I used Markup to annotate the intersecting rows and columns with common letters. These puzzles can be completed online but I'm not sure if one person's changes are common to all future versions of the puzzle.