67. In "The Return of the Prankster" Clark is a little more assertive about staying with him. While she is with him, he has to go out for a rescue. When he comes back from a major save exhausted he forgets that Lois is staying with him. He makes himself at home and Lois, brow furrowed put two and two together. Clark is Superman.
68. In "Lucky Leon," Clark attempts and fails to save Mayson in time. Lois sees the "S" through his torn shirt and very quickly surmises that Clark is Superman.
(BTW, I'm sure there are other less obvious ones in "Lucky Leon" as well.)
69. In "Resurrection": When Scardino levels the gun at Clark and says "unless you're Superman I wouldn't do that." Clark calls the guy's bluff and superspeeds out of the way of the shot while still grabbing the gun. Lois, seeing this realizes that Clark IS Superman.
CLARK: No. I'm just worried I'm a jinx.
JONATHAN: A jinx?
CLARK: Yeah. Let's face it, ever since she's known me, Lois's been kidnapped, frozen, pushed off buildings, almost stabbed, poisoned, buried alive and who knows what else, and it's all because of me.
-"Contact" (You're not her jinx, you're her blessing.)
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