In this strip of Holiday Wars, Labor Day makes a reference to some sort event that happened ten years ago in Venice. It's the first time in the webcomic that really hints that there is a large history between all the main characters.
Concerned has a lot of these. In one strip Frohman find out he can use the force (that's what he said, not me) to pick stuff up. For most of the rest of the comic, whenever he holds something it floats in front of him.
At one point, Belkar suggests selling a captured female antagonist into slavery because he "knows a guy who knows a guy". Several plot-arcs later, the party runs into said guy-his-guy-knew, Buggy Lou, as he's out catching slaves in the desert.
V's raven familiar fails to recognize her/him when s/he is transformed into a lizard. 536 strips later, he learns of his mistake.
In an early strip, Durkon lectures Hilgya on dwarves, misery, and duty, telling her how his mother taught him to take feelings like love "and bury them inna a deep dark part o' my soul and nev'r ev'r talk about 'em again." over a thousand strips later, we see his mother teaching him just this lesson, and the circumstances of said lesson.
It's Walky! celebrated its tenth anniversary (and the birth of a new character) with a Call Back to its first two strips.
According to Doc Scratch, Call Backs are a rule of Paradox Space.
And Calibornhates the frequent Call Backs and gets pissed off when Dirk notices that he's repeating phrases that other characters have used, which is a sort of meta-commentary on readers who find this practice irritating.
In 5 Color Control, Vlad and Dave's match in the Pro Tour intentionally mirrors their earlier games from earlier comics.
In General Protection Fault, after Trent sues Fred for libel, Fooker proposes breaking into his house again, like they did to clear Trudy's name. Nick, however, refuses and points out that it comes off in a new light now that they know he's a secret agent. The "To Thine Own Self" arc is based around a universe in which an alternate universe's Nick and Ki enacted a scheme their prime counterparts dreamed about in a brief arc in the early comic and took over the world.
Bob and George: Overlooking all the Running Gags, in an early strip Bob agrees to a suicidal plan with the phrase "Sure, why not, I was tired of living anyway." Fast-forward several years, and Alternate Mega Man and Bass cheerfully use the exact same justification for an equally suicidal plan. (Naturally, this being Bob And George, certain death...isn't as certain as you'd expect.)
Karin-dou 4koma: Seren makes a lighthearted promise to Mifi to let her meet Seren's captive demon lord; 88 pages and almost 2 years later, she finally does.
This strip of The Whiteboard gives a nod back to Sandy's firstpaintball game, where Rainman suggests reading a pamphlet titled "Coping with loss" after Sandy asks what to do taken out of the match by a hit, with Bandit offering one such pamphlet to a generic player he managed to sneak up on to tag out.
Zebra Girl: At the beginning of the comic, when Sandra realizes she has been turned into a demon, she calls herself a freak. Years later, when she is wondering what she exactly is, someone who had disappeared from the radar delivers this line:
Mr. Chalk: Oh Sandra. You know. You called it on day one. You're a freak.