Hmm. Can't bring it down to less than 2 per series:
TOS: Sulu & Spock.
Sulu's always struck me as the smarter member of the cast, the only one who seems to think faster than the plot (at times), and Spock, well, it's Spock.
TNG: Picard & Worf.
Picard's unfailling humanistic ethics and love of Shakespeare, Worf's strict adherence to his ways.
DS9: Quark & Garak.
As a whole, DS9 was a series that had better supporting chars than the main crew. Quark IS DS9, in many ways and Garak's appearances are always welcome, though by necessity he couldn't've been a permanent fixture.
VOY: Tuvok & The Doctor.
Easy choice, the others are either bland (Kim), mildly annoying (Paris, Kes, B'elanna, Chakotay, 7o9), unbearably annoying (Neelix) or insane (Janeway).
I liked Tuvok's brand of vulcan: he was all about logic, like all vulcans, but still differed from previous portrayals (notably Spock) nonetheless... I dare say he was better written than Spock.
The Doctor, of course, steals the show.
ENT: Phlox & Shran. Once again, easy choice, most of the ENT crew is quite bland (I was halfway through S1 before I could distinguish Trip from Malcolm!); only those two have genuine colour.