TOS:
Dreadnought
Battlestations!
The IDIC Epidemic
Spock's World
Shadows of the Sun
Best Destiny
Vulcan!
TNG:
The Children of Hamlin
Relics
Crossover
Grounded
Devil's Heart
Reunion (I Think this is the title--where Picard meets former Stargazer crewmates and one of them is a suspected killer)
DS9:
Emissary
What You Leave Behind
Avatar I and II
New Frontier: ALL OF THEM!
New Frontier is one series that I'd love to see come to TV, either as a TV movie or mini-series. Those characters rock.