I once did a thread at TZ about scenes we know happened but weren't shown, some of which included Superman first putting on his costume and John getting the GL ring.
AMAZO's ultimate fate.
Supergirl switching minds with Talia, Darkseid switching minds with Sam Lane, and Static Shaq switching minds with Steel.
Mr. Mxyzptlk feeling lonely (after reading this - http://www.msnbc.msn.com/id/12371978/), visits Carl Rossum and turns Bat-Mite into an imp like him (voiced by Bobcat Golthwait). They team-up to bug the Justice League.
Superman telling Lois who he is.
Ben Savage voicing a Robin Beyond, and he and Terry Bats go into the past and team with Hawk & Dove.
Flash and Linda kissing, John and Shayera kissing.
Speaking roles for Dr. Mid-Nite, Ice, Hourman, and on-screen appearances by Blue Beetle, Firestorm, and Plastic Man.
An episode where Flash, Green Lantern, J'onn, Black Canary (or maybe Wonder Woman) and Aquaman (the founders in the comic) team-up (like the original five on X-Men Evolution did)
Some real Batman/Nightwing resolution.
Some real Zeta Project resolution.
Going back and digitally inserting Riddler and Scarecrow into the Legion's headquarters and Aquaman between Green Arrow and Black Canary in "Destroyer".
BLACK ADAM!!! (he was mentioned)
Ehhh, there's probably more, but that's all I can think of. Feel free to add any.