I like that episode where the Enterprise gets infected by that ancient virus and then in the end the big ' it's so crazy it just might work' plan is to basically just reformat the computer.
To be fair, that was the experimental neural gel pack circuitry voyager had. Supposedly faster than normal circuitry but also organic and susceptible to infections and disease
I bet once Starfleet reviewed all of Voyager's mission logs, they either vaccinated existing bio-neural gel pack ships against cheese and/or, if still in production, added "expose to various types of cheese" to their unit tests. lol