I loved 25th and JR back when they were released. Except the space fights which I remember being ridiculously hard. I think I never actually beat those games. In one of them you had to fight a copy of the Enterprise AND two romulan or klingon ships simultaneously. I never got past that fight.
I think I still have JR somewhere, but someone borrowed 25th from me and never gave it back, no clue who it was either. That was many years ago.
Never played ST Academy, so I don't know whether I like that one, but I recently bought a used "ST: A Final Unity" box including a signed portrait of Marina Sirtis (yay!), and that game is also great. Probably the pest ST adventure.