I think one of the reasons that Star Trek has done as well for its self as long as it has is related to it's treatment of women. You may not know this but in the original series the pilot had all of the female officers wearing the same uniform as the men. The censors wouldn't hear of it and so the mini dress was donned. I personally kind of wonder if the mini dress was there specifically to screw with the censors who didn't want the women in pants.
No pants? Fine, how about Uhura's bright red panties?
Now the original Star Trek series hasn't exactly endured well in my opinion. Uhura didn't really have a job, Chekov, Scotty, and Sulu occasionally drift into the politically incorrect, and everyone is surprisingly vulnerable to Styrofoam. But I personally give it a pass because they still did something amazing for that time period and honestly I think changed television forever. So although no one from the original series will be on this list, it's important remember origins and what Star Trek did for women in television. Starting off with that attempt of female officers, on the bridge, with the same rank as some of the male officers.
As a warning the discussion about why I like these characters will have spoilers for the show, but now on to some of my favorite female officers:
Over arching love of these characters comes from the fact that each of them is single for a long time on the show, and these characters never feel like they need a man. They're awesome on their own and when they do get together with people it's only to add to their already rich lives, not to save them or to complete them.
Now of course there are more, but these are my favorite female Star Fleet officers. If you haven't checked out these awesome ladies, I highly recommend it. Yes some of the episodes are bad and cheesy, but not all of them and these characters are worth it in my opinion.