If you're including Riker/Troi I'll add them to my list too. The only reason I didn't is because I think of them more as a TV/Movie couple than a Trek Lit one. Oh, and I completely forgot about Chakotay/Janeway, it didn't last long, but what little there was of it was great.
Hernandez/Inyx is pretty good.
I'm a sucker for Trip 'n T'Pol.
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