"The Jihad" is an awesome story. No contest.
"The Jihad" fully utilizes the advantages of animation to tell a story that would have been practically impossible as live-action. Only today with cgi could something like "The Jihad" be done.
The Skorr T'char is an awesome alien design, but wholly impossible as live-action back when TOS and TAS were made. Today it would be wicked to see something like that.
"The Lorelei Signal" isn't horrible, but it's fluff compared to "The Jihad." "The Lorelei Signal" is noteworthy for two things, though: it shows us female Starfleet personnel in action as well as Uhura assuming command, and the story's basic idea predates TNG's "Man Of The People" by about twenty years.