My favourites:
1. The Doctor - great development over the entire series and a very entertaining character to watch
2. Janeway - she got the job done and was determined to get her crew home no matter what stood in her way. That takes some serious balls (in a manner of speaking). She was also resourceful and believed that there was a solution to any situation, now that's the thinking of a scientist!

I think Janeway is awesome and she's definitely my favourite captain, shame that some of her actions were contradictory though.
3. Seven of Nine - I love the idea of a character searching for humanity; it was a really unique storyline that I found interesting. My only complaint is that I felt like Seven was introduced into the show for visual appeal, and that is not what her character is about.
B'Elanna, Tom and Tuvok are the next to follow. I like them as characters and they each have their own fascinating personality quirks and small arcs that add to the story, but their stories didn't grab me as much as the others.
At the bottom are Harry and Chakotay. I'm just generally disappointed by the writing for these two because it left them severely under developed as characters (Harry was an ensign for seven years for crying out loud!) and Chakotay never really found his place as a character, which is really too bad as I feel like so much could have been done with both of these characters.
On a side note, I actually liked the episode 'The Fight' as I felt like it finally gave us some introspection into Chakotay's character.