My favourites (in no particular order):
Chain of Command - Great acting by Patrick Stewart in those intense torture scenes. Was also fun to see Captain Jellico and how the crew reacted to him.
Tapestry - I love Q episodes, but this one was a bit different. Q wasn't just messing around because he was bored. He actually taught Picard a lesson, in his own way. Great chemistry between Q and Picard as always and a charming story.
Best of Both Worlds - Epic. Borg are awesome. Patrick Stewart is awesome. This two-parter is awesome.
Frame of Mind - Great acting by Frakes. Unique, strange story that keeps me glued to the screen. Had no idea what was going on the first time I saw this lol.
All Good Things - Fitting end to a great show. The three timeline idea was very cool. Lots of nice touches; bringing back Q, the trial of humanity, the refitted Enterprise D and of course the poker scene at the end. Best finale of any Trek show, easily (DS9 had a pretty good finale I suppose).