Zek/Moogie (Lameness that hurt any that either character had going for them...which wasn't much to begin with.)
Chakotay/Seven, a romance as flat as a pancake...made worse by it's series finale factor "SEVEN dies and Chuckles is never the same again!"
Ezri/Worf/Bashir (Ezri fucking broke the fucking Trill rules and should have that slug yanked from her and left to die...okay, that's harsh...)
Gun/Fred (why did Whedon push the tough guy/geeky girl angle...is he just a self-hating nerd? Or was it that didn't know what to do with Gun?)
Mulder/Scully, no one has the guts to say it, I guess. The series was reduced to 'shipper crapola...IT'S MOONLIGHTING
WITH ALIENS...OF COURSE THEY'LL EVENTUALLY "DO IT". (Okay, I've learned to live with it...)
David Addison/Maddie Hayes, they "did it" and the show immediately turned to crap.
I have mixed feelings about Odo/Kira...him loving her, yes. Her loving him romantically...not sure it should've been.