1990: Crossword Concerto (song) by Robert Wells, album Rhapsody in Rock II- Landscape Painted With Tea (book) by Milorad Pavić; "A failed architect's search for his father, an officer who vanished in Greece during World War II, becomes a labyrinthine puzzle, inextricably bound to the history of the ancient monastery on Mount Athos". It's organized as a crossword puzzle: "Readers may approach the book chronologically by reading only the 'Across' sections, or less chronologically and with more digressions by reading the 'Down' sections. Either strategy gradually reveals the story of a soul-searching architect who roams a labyrinth of meditation and memory." "In ergodic literature, nontrivial effort is required to allow the reader to traverse the text"
- More Than Words (song) (video; 4:17) (wikipedia) by Extreme, album Pornograffitti;
lyrics: "How easy it would be to show me how you feel; More than words is all you have to do to make it real" 
1991: Nothing Turned Out Right (song) by Demon, album Hold On To The Dream;
lyrics: "So I walked in the sunshine / And suddenly it started to rain / So I reached for the crossword
But couldn't find where I'd left my brain / It's just one of those days / When nothing turns out right"- 1992: Bambi Is a Stag and Tubas Don’t Go ‘Pah-Pah’: The Ins and Outs of Across and Down
NYT (Sun) Crossword 50th Anniversary - Happy Phantom (song) (video; 4:17) by Tori Amos, album Little Earthquakes;
lyrics: "They say Confucius does his crossword with a pen / I'm still the angel to a girl who hates to sin" 
1993-present: Will Shortz: 4th NYT crossword editor- 1994: Crazy Crosswords (Australia) (TV game show; 1994-1996)
- Jigsaw (song) (video; 4:09) by Love Spit Love, album Love Spit Love;
lyrics: "i've got to get this crossword done / of everything you've said / all the one way conversations
words that i forget / and it would be so easy to see / if i could be there now" 
1995: Crossword Blues (song) (video; 6:07; lyrics: 4:10-) by Rob Tognoni, album Stones and Colours; MayasMix @ 89:50
lyrics: "lately I've been learnin' to do the crossword everyday / it's just one of those things I'm gonna need to while my lonely hours away"- Oliver's Travels TV; PBS; "When Oliver (Alan Bates) ... is laid off by his university, he resolves to visit Aristotle, a famous compiler of crossword puzzles. When Oliver discovers that Aristotle's home has been ransacked and Aristotle is nowhere to be found, ..."; Guardian article
1996: NYT adopts Across Lite application & .puz format- Election Day: The clue to the middle answer across the grid was "Lead story in tomorrow's newspaper." The answer appeared to be CLINTON ELECTED. Because of intentional ambiguity in the crossing clues, however, the answer could also have been BOB DOLE ELECTED. Either answer fitted. For example, the crossing clue Black Halloween animal could have been either BAT or CAT, with the C for CLINTON or the B the start of BOB DOLE. "It was the most amazing crossword I've ever seen. As soon as it appeared, my telephone started ringing. Most people said 'How dare you presume that Clinton will win!' And the people who filled in BOB DOLE thought we'd made a whopper of a mistake!" ~Will Shortz.
- 1997: Crossword Weaver: first commercial computer software program for creating crossword puzzles.
1998: USPS issues commemorative crossword stamp- Mercury Rising (movie); "An autistic 9-year-old boy cracks the U.S. government's top-secret code when an unapproved test matrix gets published in a crossword magazine."
- marriage proposal puzzle [NYT] Will Shortz Discusses (video: 2:56)
included 20-A: "1729 Jonathan Swift pamphlet": A MODEST PROPOSAL; 56-A: "1992 Paula Abdul hit": WILL YOU MARRY ME.
others: Newsday (1998); Eugene Weekly (2005); Washington Post (2011) (video: 3:50) 
1999: A Clue for the Puzzle Lady (mystery, 1st in Puzzle Lady series) by Parnell Hall; synopsis: "Amateur sleuth Miss Cora Felton, an eccentric, nationally-syndicated crossword puzzle columnist whose craving for trouble has increased with age. When the body of an unknown teenager carrying a cryptic, crossword-like message is found in the local cemetery". Other books: Last Puzzle and Testament, Puzzled To Death, ...- Kill the Man (movie);
"Guy: What are you doing in my parking lot?
Bob Stein: Murder.
Stanley Simon: Yeah, handsome guy too.
Guy: The corpse just moved!
Stanley Simon: They tend to do that sometimes. I once saw a man finish a crossword puzzle after being shot five times.
Bob Stein: Sunday edition too." 
The Crossword Murder (mystery) by Nero Blanc from Crossword Mysteries (series)- Nobody Knows Anybody (Nadie Conoce a Nadie) (movie); "Simón (Eduardo Noriega), a crossword-puzzle writer, receives a cryptic message threatening him with death if certain words don't appear in his puzzles."
- Your Dictionary (song) (video; 3:30) by XTC, album Apple Venus Volume 1;
lyrics: "H-A-T-E -- is that how you spell love in your dictionary...There are no words for me inside your dictionary" - The Story of Us (movie); Ms. Pfeiffer's character designs crossword puzzles. Mr. Willis goes from skepticism that anyone can make a living at such an activity to examining, later in his marriage, his wife's puzzles for insights into their relationship and its decidedly murky prospects; he starts to see her crosswords as secret messages. Wikipedia; NYT