What antogonist/s would you consider the main villain for each of the crews?
TOS-It's between Khan and the Klingons, but you've got to go with the Klingons based on the frequency of their appearances, plus being the villains of three of the features, and at least two episodes that would be considered classics (Errand of Mercy and The Trouble with Tribbles)
TNG-It's a tossup here between Q, the Borg, and the Romulans. The Borg were in two two part epiodes, including the most famous episode in the series, plus several other episodes and the best TNG movie. Q was in both the series finale and premiere, introduced the Borg, and was in what is generally considered one of the best shows in the series in "Tapestry". I'm going to eliminate the Romulans, because they don't really have a "signature" moment in the series. Unification and The Gambit would come closest. I'll go with Q, since he was on the show more often, and really was the perfect foil for Picard.
Ds9-Obviously it's between the Cardassians and Dominion. You could really just consider them one villain. I'd go with the Cardassians, since Gul Dukat is the most famous individual villain on the show, and so much of it revolved around the aftermath of the Bajor occupation.
Voyager-The Borg. Really not a debate. I wish it would've been the Hirogen
Enterprise-You could go with the Xindi, you could go with the Suliban/Future Guy, and you could even go with the Klingons. If you show had stayed on a few more years it would've probably been the Romulans. I'll go with the Xindi, just because they were obviously the most frequent villain on the show overall, and the Xindi arc was my favorite part of the show.