When initially commissioned by NBC to write a pilot episode for Star Trek in 1964, Gene Roddenberry submitted three story outlines. Out of these three, the one that became "The Cage" was chosen by the network and filmed.
NBC rejected the pilot, but because they had chosen that story themselves from the three choices (and the story was perceived as the main source of the problems), they ordered a second set of three scripts for a second pilot, and the rest is history.
All three of these second-attempt pilot scripts eventually became episodes of the series: "Where No Man Has Gone Before", "Mudd's Women", and "The Omega Glory".
But what were the other two pilot story treatments rejected in favor of "The Cage"? I've read countless articles, "making-of" books, etc. and never seen an answer to this. Were they eventually revised and made as episodes of the show as well?
Given the "Law of Conservation of Stories" that episodic television is subject to (namely that -- due to budget crunches, tight schedules, writer strikes, and the like -- every remotely-workable plot idea will eventually be pulled out and produced as an episode), it seems unlikely that they were completely scrapped.