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Beam Me Up, Scotty!: In-universe; in a realistic touch, Joe quotes The Godfather off-hand to Kathleen, but misquotes it as "I didn't know who you were with." It's actually "You should've told me your boss was Corleone."
Playing Against Type: Steve Zahn and Dave Chappelle play low-key comic relief as opposed to their more over-the-top roles.
This being a film where people use computers in 1998, you will of course hear the sounds of dial-up modems connecting to America Online 4.0 (released that summer) on laptops that, compared to Netbooks and even tablets today, look incredibly bulky. In addition, the use of instant messaging, chat rooms and email, rather revolutionary at the time, is now rather overshadowed by the rise of social networking, audio/video chat, and text messaging on mobile phones. The anonymous pen pals premise might be a tad harder to pull off today in comparison.
More early-AOL residue: During the one sequence using Instant Messenger, both characters type in far more into the windows than what most people do today, who prefer to break up long blocks of text across several IMs.
These days online book retailers and e-booksellers are the ones forcing mega-bookstores out of business, making Fox Books' dominance a bit hilarious in hindsight.
Those Two Actors: Tom Hanks and Meg Ryan. Incidentally, this movie came out five years after Sleepless In Seattle and critics made note of the vaguely similar plots—in the first film, they don't even meet until the end while in this one, they meet right away but spend a good portion of the film unaware that each is the others online paramour.
Throw It In: When Tom Hanks accidentally closed the door on the string of the balloon leaving The Shop Around The Corner, he popped it open for a moment to free the balloon and added the line, "Good thing it wasn't the fish!"