My big problem with "The Practical Joker" -- aside from the juvenile behavior of the crew -- is that it uses sitcom-amnesia logic to cure the problem. Why would a second trip through the cloud fix the computer instead of just making it worse? As a child I figured it was because they flew through it in the other direction, but that's a pretty stupid explanation. Also, the episode's portrayal of the effects of nitrous oxide is cartoony and inaccurate.
I figured the thing that possessed the Enterprise computer never wanted to be there. It was snagged somehow as the ship first passed through, and so when the ship returned to it's home it GTFO ASAP.
I thought "The Practical Joker" was probably an inspiration for Next Gen's "Lonely Among Us"