When you are looking after 700 episodes, everyone has it's own favorite list of episodes.
TOS, in my opinion, has the most (storywise) best episodes, after then TNG. VOY has it's highlights, but not even great then TOS/TNG. DS9 has a great overall storyline, but not in terms of single storys. ENT doesn't intrest me like TOS/TNG and VOY. Sadly, the show was turned down after it's going better on Season 3 and even more Season 4.
Here is my TOP 10 list:
1. The Best of Both Worlds (TNG)
2. Amok Time (TOS)
3. The City on the Edge of Forever (TOS)
4. Cause and Effect (TNG)
5. Yesterday's Enterprise (TNG)
6. All Goods Things (TNG)
7. The Doomsday Machine (TOS)
8. Mirror, Mirror (TOS)
9. Future's End (VOY)
10. Year of Hell (VOY)