Has to be Tuvok, no question about it for me.
As for the others:
Chakotay - Without Janeway there to tell him what to do he'd be lost
Paris - A decent pilot, not exactly leadership material
Kim - Sorry, but no one takes a seven year ensign seriously
Seven - I'm actually surprised she was never given command, seeing as how she did everything else onboard
EMH - I don't trust holograms, anyone that can be reprogrammed or deleted with a single command isn't suitable for the starboard side seat.
Commander Austin Harris, First Officer, Deep Space Nine (by FltCpt. Bossco)
8.01 - Darkest Before Dawn
(Chapter 8 added, 12/09/2015)