From A Modest Destinythe main character learns how to control his shadow as a joke. It isn't mentioned again until he's facing down the Big Bad, when he uses this power to defeat him
Roy's grandfather takes the time to teach him a special move to disrupt spellcasting while they chill in the afterlife. The likelihood of this not coming back to play an important role later is approximately nil.
Sadly, it gets wasted against an illusionary Xykon inside of a Lotus-Eater Machine.
Earlier in the series, when Vaarsuvius is polymorphed into a lizard, s/he finds that only three of his/her spells will work in this new form: Hold Portal, Feather Fall, and Suggestion, all of which seem useless. Naturally the party find themselves stumbling over a steep slope, requiring Feather Fall, and then meet a dragon who speaks Lizard and is therefore a valid target for Suggestion. In a subversion, Hold Portal doesn't work when it could have been used because there are no portals around to hold.
This becomes a bit of a Chekhov's Boomerang later when Vaarsuvius is paralyzed during an attack but has the foresight to have these spells memorized just in case a similar circumstance would occur again.
We learn during Schlock's origin story that carbosilicate amorphs were evolved from advanced data storage systems. This becomes important in another story arc much later when a piece of Schlock is used to rescue a rogue A.I.
In Venus Envy, Zoe's Tai Chi comes in useful when Nina comes at her with a knife. Would have worked out great if not for the fact Zoe was holding something herself afterward.
In El Goonish Shive, it took nearly eight years to explain how Susan made a sword appear back during the Sister arc.
In episode 176 of Roommates, we see Jamie put to use the dramatic rope skills he learned from Erik all the way back in episode 68, over 32 months prior.
In Too Much Information, we learn Ace's mom is still in the armed forces. We learn she's a language expert. We learn she's picked up a few extra languages recently. After years of set-up, we finally learn what she really does: she is on an SG team for the Stargate program.
