I'm in the middle of doing my manual transmission fluid change. I don't know when the last time it was changed and it came out really dark. I was wondering if I should fill it with motor oil and drive around for a few miles and then drain and fill with the Honda manual transmission fluid?

Would there be any gain or should I just fill it with Honda fluid now and leave it at that?

 

Just fill it with Honda MTF. Drive on fresh MTF for a few thousand, then check the color again.

 

This. Though, depending on the year, you don't need Honda MTF and regular motor oil is called for by the service manual (for 92-95). Definitely do NOT put anything else in there to try to "wash" it out. Just empty and fill with oil, and repeat if desired.