I think "The Thaw" is a great Voyager episode that really creeped me out. The Clown is a worthy addition to Trek villains. His only downside was that, as an existential threat, he was limited in scope to his little virtual reality and the people connected to it. But he was malevolent, really like no other villain in Trek lore. Hard to believe it was sweet Lenny Kosnowski.
On a different note altogether, I found the Automated Personnel Units in "Prototype" to be intriguing villains. Making their power cells impossible to reproduce, in order to guard against the threat that they represent by nature, was a nice touch.
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