Leonard and Sheldon in “The Hamburger Postulate”

What did Penny mean, "you'd make a cute couple"?

Well, I assume she meant that the two of you together would constitute a couple that others might consider cute. An alternate, though somewhat less likely interpretation is that you could manufacture one. As in, "Oh, look, Leonard and Leslie made Mr. and Mrs. Goldfarb! Aren't they adorable?"

If Penny didn't know that Leslie had already turned me down, then that would unambiguously mean that she, Penny, thought I should ask her, Leslie, out, indicating that she, Penny, had no interest in me asking her, Penny, out; but because she did know that I had asked Leslie out, and that she, Leslie, had turned me down, then she, Penny, could be offering me consolation - "That's too bad, you would have made a cute couple..." - while thinking, "good, Leonard remains available."

You're a lucky man, Leonard.

How so?

You're talking to one of the three men in the Western Hemisphere capable of following that train of thought.

Well, what do you think?

I said I could follow it, I didn't say I cared.