I made up a couple of crossword puzzles years ago for copy editing trainees, violating all the rules in the process. It ain't easy but it's a lot of fun.
Speaking of rules, I didn't know this until recently, which shows you how much I was paying attention. From Wikipedia and mentioned in the documentary "Word Play."
Another tradition in puzzle design (in North America and Britain particularly) is that the grid should have 180-degree rotational symmetry, so that its pattern appears the same if the paper is turned upside down. Most puzzle designs also require that all white cells be orthogonally contiguous (that is, connected in one mass through shared sides, to form a single polyomino).