Well, my favorite show depends on when you ask me. I did enjoy them all in different way. Yes, I even like Voyager.
My favorite Episode of TOS had to be the Salt Monster. For TNG, the two top ones are when Picard lives out his entire life in "a village" but it turns out to only be a couple seconds of down load form a probe. The second, of course has to be the death of Tasha Yar. That was hilarious.
For Voyager, my favorite episode was the one where Kess aged backwards. That woman has a voice that could melt stone. I mean that in a good way. Of course, the Year From Hell story line was good, too.
I don't really have a favorite Enterprise eopisode yet. There were so many good ones. The mirror universe was pretty awesome, though.