The first, "The Cage," was rejected by NBC for being "too cerebral" (ah, some things never change).
The second, "Where No Man Has Gone Before," replaced the actor who played the captain with William Shatner and was more action driven. That pilot had an alternate version which was largely lost and has never aired. Apparently, a film collector in Germany acquired the print and "recently brought it to the attention" of CBS/Paramount. CBS is now releasing this version on Blu-ray Dec. 15.