Tokath (TNG, Birthright). A "man protecting his family," and at Khitomer showed far more mercy to his Klingon adversaries than I would have expected any Romulan to.
Damon Bok (TNG, the Battle). Guy's son was killed and it drove him over the edge, and this also shows us that Ferengi DO care about more than ledgers. And the briefly seen Kazago gets honorable mention for the most likable Ferengi I can remember.
This may sound crazy, but Admiral Satee (TNG, the Drumhead)? She was malevolent alright, but I really felt bad for her when she self-destructed. But....naaa. Too dislikable.
Bruce Maddox (TNG, the Measure of a Man) is definitely an adversary of sorts for the episode, but ends very sympathetically for his rueful and somewhat stunned acceptance of some truths (or at least big questions) about Data.
It is hard not to feel bad for Ben Finney (TOS, Court Martial).
Horta (TOS, Devil in the Dark).
The Grups in Miri. How can you not feel horrified pity for them, especially after the tricycle scene? "It's broken...fix...please fix it..."
Violent Kirk (TOS, the Enemy Within). Yes, Rand. But really you're not moved by "I want to live! I want to live!"? It isn't like he is really responsible for what he is, either. He's NOT a full human being who actually understands the concepts of right and wrong, or even of not fulfilling every impulse, by dint of being this distilled archetype of violence created by the transporter.
Mirror Spock (TOS, Mirror Mirror).
Gary Mitchell (TOS, Where No Man Has Gone Before). That brief moment on Delta Vega when his eyes return to normal is enough to remind us that this is Gary, Kirk's good buddy. He goes pure megalo, but I do feel bad for him anyway.
Kruge (so kidding--this is of course the poster boy for nonsympathy).