Throw It In: There are probably a bunch, but one is the unscripted chair malfunction in the moon base.
Doctor Evil's "shh"ing of Scott was made up on the spot and went on to become a running gag.
Austin's one-liners when the guard was killed by ill-tempered mutant sea bass were the result of Mike Myers forgetting his scripted lines.
In the opening dance sequence of The Spy Who Shagged Me, one of the synchronised swimmers emerges from the water with her fluffy pink hat accidentally covering her eyes.