TOS is the classic that everyone tries to emulate, however I would have to say TNG. The strength of TOS lies in how well the on screen personas melded. We know the off screen relations werent perfect, but just like another Desilu production (I Love Lucy) where Fred and Ethel could not stand each other in real life, they played great together.
TNG moved the franchise forward well beyond Kirk, Spock, McCoy and company. It also had more years to mature the crew and let them grow.
Although this is heresy, Berman and Braga established far more of Trek mythology through TNG, DS9, and Voyager than Roddenberry. Gene invented the universe, Berman and Braga populated it.
Now, of course, there were some real screw ups with ENT, however the last 2 seasons began to rectify some. Too bad it didn't last another season or two (if only to see Porthos BITE the fat ass creeper doc, who always reminded me of a child molester)