24 Hour Museum: Online crossword puzzle themed around museums, galleries, and culture. Also offers a printable version.
BestCrosswords.com: Free crosswords on a daily basis.
Canadian Criss Cross: Canadian themed puzzles in Java.
Crosswords: Online crosswords created automatically.
Crosswords and Word Puzzles: Find online crosswords, access software to write your own puzzles. Includes logic problems, palindromes, cryptics, and foreign-language crosswords. From About.com.
Dowedo.co.uk: Offers archive of puzzles in various sizes, solving software, and a crossword builder.
eDigg.com: Simple puzzles on a variety of themes.
EJ's Crossword Showcase: Crosswords, cryptic crosswords, and acrostic puzzles.
FreeWorldGroup.com: Grouped by categories with varying levels of difficulty.
Fwend.com Weekly Crossword: A weekly interactive crossword. Easy navigation with mouse or arrow keys. [Requires Java]
Goobix Crosswords: Offers 3x3 and 4x4 crosswords.
Grosswords: Rude crossword puzzles: Adult-themed and crude puzzles.
iGameFan.com: Online games and activities, specializing in crosswords.
Infoplease Weekly Interactive Crossword: A thematic puzzle. [Requires Java]
Motor-Cross Automotive Crossword Puzzles: Interactive java crossword puzzles relating to the automotive community.
Online Crosswords: User-submitted puzzles. [Requires Java]
Oxbrain.com: Illustrated adventure stories with Java-based themed crosswords complementing the storyline.
Thinks.com: Many puzzles to choose from: crosswords, anagrams, doublets, trivia, math and word searches.
TwoPaths.com: Puzzles with Biblical themes. Solve on-screen or print.
USA Today Crosswords: Daily Flash puzzle offered at two skill levels. Includes archive of past puzzles.
Webber's Anagram Crosswords: Crossword puzzles in which clues are anagrams.