The Crossword Constructors Forum is an excellent site with plenty of links to daily crossword sites, reference sources, and other crossword related material.
A cryptic three dimensional crossword is at http://world.std.com/~wij/puzzles/tetra.html, it was made by William Johnson.
A free daily crossword is available at Houston Chronicle Interactive.
Ray Hamel has put together a listing of over 200 Crossword Links. Ray has had many crosswords published.
The Puzzle Gallery contains many crosswords in Across Lite format.
A fantastic Crossword Construction program is available from Antony Lewis. I use his program constantly -- I like watching it try to fill in nearly impossible grids. Here are some examples of some interesting fills the program has come up with:
All of these puzzles have various problems that would keep them from being good for places like The New York Times. Obscure words, boring themes, and an excess of black squares are things to avoid when crafting a crossword... even if you get help from a crossword compiler!