Daily List suggested by bgoul030.
30) Luther Sloan
The appearance of this covert Section 31 agent who made life miserable for Julian Bashir on Deep Space Nine blew the lid off of Starfleet's dark side. His outlook -- like that of many characters on DS9 -- eschewed viewing the world in and black and white to instead focus on the shades of gray that keep society functioning.
29) Reman Viceroy
28) John Frederick Paxton
Enterprise had many problems, but quality acting was never one of them. The series' most memorable foe (only memorable foe?) was John Frederick Paxton, a bigot who wanted Earth to be free from non-human life forms. Peter Weller's portrayal infused the character with some genuine menace that made for some captivating television.
27) Lursa and B'Etor
What's the greatest legacy of the Duras sisters? How the pair caused endless grief for Worf, or how they introduced an entire generation to Klingon breasts?
25) The Pah-Wraiths
24) The Vidiians
The old urban legend about kidney thieves got a sci-fi makeover in the form of this race from Star Trek: Voyager who were inflicted with a disease that forced them to harvest the organs of healthy aliens in order to stay alive. Eventually the show revealed that the illness ravaging the Vidiian people was cured, thus shattering viewers hopes of seeing a gnarly Chakotay on the bridge.
Apparently, even in the 24th century BP is fucking shit up.
22) Worf's Zit
21) The Devidians
The Devidians were the alien race that were ingesting the life energy of dying San Franciscans in the "Time's Arrow" Star Trek: The Next Generation two-parter (the episodes where Data loses his head in the 19th century and Mark Twain gets into hi-jinks). Their ability to effortlessly travel through time and space to prey on weaker civilizations makes them one of the more interesting races to pop up on the series. Sadly, an exploration the Devidians' motives was glossed over by the writers so that viewers could see more madcap antics by the theater troupe the Enterprise crew was posing as. Come to think of it, maybe all Trek-related comedy should be up higher on this list.
Poor Lore. He just wanted to get the attention from Dr. Soong that Data did, but instead his superior brother who got all the breaks and chicks shot and deactivated him and before stealing his emotion chip. So who really is the bad guy here?
A big horned Space Yeti? Fuck and yes.
18) The "Conspiracy" Aliens
The first season of Star Trek: The Next Generation was shaky at best. A high point of the year was the "Conspiracy" episode in which Picard and company encountered some delightfully shitty stop-motion aliens who apparently lived in Trapper Keepers. Jump to 5:28 in the above clip and enjoy some special effects that make Belial in Basket Case look like a Lucasfilm creation by comparison. Even though they are extraordinary cheesy, the creatures are so shithouse bonkers that you have to admire them.
This is a bit of a cheat because Moriarty wasn't a villain created specifically for Star Trek, but since one of the greatest bastards ever in pop culture turned up on the show it seems fitting that he be featured here as well. And speaking of holograms...
16) The Holodeck
Even though it's not a sentient being, too much bad shit goes on in the Holodeck for the Federation to not see it as a threat. Be it games of Parrises Squares or Wild West whores who look like Data, there's always something crazy going in there. On board the Enterprise you can't get Romulan Ale, but you can fuck simulations of your crewmates and get in all sorts of danger on the Holodeck at any given time. That just doesn't seem right.