There are so many good episodes I'd have a tough time squeezing them into a top 50, but the top 10 I am fairly sure of:
1. Best of Both Worlds I and II
2. The Chase
5. The Inner Light
6. The Survivors
7. The Wounded
8. Q Who
9. Where No One Has Gone Before
10. All Good Things..
In particular, The Chase has moved up the list over the years. It gets better all the time despite the TOS-style production design misfire at the end. Its one of the touchstone episodes of all of ST, encompassing everything Gene wanted for ST. It also would make the BEST springboard for a future ST movie, since the events in the ep were so monumental to evolution in the galaxy. It even inspired me to write a movie synopsis, and I am by no means a fanfic enthusiast.
Other episodes of major note to me:
Measure of a Man
Birthright Part 1
ah damn, and many more.